80 results on '"Janelle R. Thompson"'
Search Results
2. Gut Ruminococcaceae levels at baseline correlate with risk of antibiotic-associated diarrhea
- Author
-
Xiaoqiong Gu, Jean X.Y. Sim, Wei Lin Lee, Liang Cui, Yvonne F.Z. Chan, Ega Danu Chang, Yii Ean Teh, An-Ni Zhang, Federica Armas, Franciscus Chandra, Hongjie Chen, Shijie Zhao, Zhanyi Lee, Janelle R. Thompson, Eng Eong Ooi, Jenny G. Low, Eric J. Alm, and Shirin Kalimuddin
- Subjects
Health sciences ,Pathophysiology ,Microbiome ,Science - Abstract
Summary: Antibiotic-associated diarrhea (AAD) affects a significant proportion of patients receiving antibiotics. We sought to understand if differences in the gut microbiome would influence the development of AAD. We administered a 3-day course of amoxicillin-clavulanate to 30 healthy adult volunteers, and analyzed their stool microbiome, using 16S rRNA gene sequencing, at baseline and up to 4 weeks post antibiotic administration. Lower levels of gut Ruminococcaceae were significantly and consistently observed from baseline until day 7 in participants who developed AAD. Overall, participants who developed AAD experienced a greater decrease in microbial diversity. The probability of AAD could be predicted based on qPCR-derived levels of Faecalibacterium prausnitzii at baseline. Our findings suggest that a lack of gut Ruminococcaceae influences development of AAD. Quantification of F. prausnitzii in stool prior to antibiotic administration may help identify patients at risk of AAD, and aid clinicians in devising individualized treatment regimens to minimize such adverse effects.
- Published
- 2022
- Full Text
- View/download PDF
3. Engineered microbial biofuel production and recovery under supercritical carbon dioxide
- Author
-
Jason T. Boock, Adam J. E. Freedman, Geoffrey A. Tompsett, Sarah K. Muse, Audrey J. Allen, Luke A. Jackson, Bernardo Castro-Dominguez, Michael T. Timko, Kristala L. J. Prather, and Janelle R. Thompson
- Subjects
Science - Abstract
End-product toxicity, culture contamination, and energy efficient product recovery are long-standing issues in bioprocessing. Here, the authors address these problems using a fermentation strategy that combines microbial production of branched alcohols with supercritical carbon dioxide extraction.
- Published
- 2019
- Full Text
- View/download PDF
4. Isolation, Development, and Genomic Analysis of Bacillus megaterium SR7 for Growth and Metabolite Production Under Supercritical Carbon Dioxide
- Author
-
Adam J. E. Freedman, Kyle C. Peet, Jason T. Boock, Kevin Penn, Kristala L. J. Prather, and Janelle R. Thompson
- Subjects
supercritical carbon dioxide ,bioprospecting ,strain isolation ,Bacillus megaterium ,bioprocessing ,bacterial spore germination ,Microbiology ,QR1-502 - Abstract
Supercritical carbon dioxide (scCO2) is an attractive substitute for conventional organic solvents due to its unique transport and thermodynamic properties, its renewability and labile nature, and its high solubility for compounds such as alcohols, ketones, and aldehydes. However, biological systems that use scCO2 are mainly limited to in vitro processes due to its strong inhibition of cell viability and growth. To solve this problem, we used a bioprospecting approach to isolate a microbial strain with the natural ability to grow while exposed to scCO2. Enrichment culture and serial passaging of deep subsurface fluids from the McElmo Dome scCO2 reservoir in aqueous media under scCO2 headspace enabled the isolation of spore-forming strain Bacillus megaterium SR7. Sequencing and analysis of the complete 5.51 Mbp genome and physiological characterization revealed the capacity for facultative anaerobic metabolism, including fermentative growth on a diverse range of organic substrates. Supplementation of growth medium with L-alanine for chemical induction of spore germination significantly improved growth frequencies and biomass accumulation under scCO2 headspace. Detection of endogenous fermentative compounds in cultures grown under scCO2 represents the first observation of bioproduct generation and accumulation under this condition. Culturing development and metabolic characterization of B. megaterium SR7 represent initial advancements in the effort toward enabling exploitation of scCO2 as a sustainable solvent for in vivo bioprocessing.
- Published
- 2018
- Full Text
- View/download PDF
5. Corrigendum: Characterization of Metagenomes in Urban Aquatic Compartments Reveals High Prevalence of Clinically Relevant Antibiotic Resistance Genes in Wastewaters
- Author
-
Charmaine Ng, Martin Tay, Boonfei Tan, Thai-Hoang Le, Laurence Haller, Hongjie Chen, Tse H. Koh, Timothy M. S. Barkham, Janelle R. Thompson, and Karina Y.-H. Gin
- Subjects
comparative metagenomics ,antibiotic resistant genes ,wastewaters ,hospital ,municipal ,water body ,Microbiology ,QR1-502 - Published
- 2018
- Full Text
- View/download PDF
6. Characterization of Metagenomes in Urban Aquatic Compartments Reveals High Prevalence of Clinically Relevant Antibiotic Resistance Genes in Wastewaters
- Author
-
Charmaine Ng, Martin Tay, Boonfei Tan, Thai-Hoang Le, Laurence Haller, Hongjie Chen, Tse H. Koh, Timothy M. S. Barkham, Janelle R. Thompson, and Karina Y.-H. Gin
- Subjects
comparative metagenomics ,antibiotic resistant genes ,wastewaters ,hospital ,municipal ,water body ,Microbiology ,QR1-502 - Abstract
The dissemination of antimicrobial resistance (AMR) is an escalating problem and a threat to public health. Comparative metagenomics was used to investigate the occurrence of antibiotic resistant genes (ARGs) in wastewater and urban surface water environments in Singapore. Hospital and municipal wastewater (n = 6) were found to have higher diversity and average abundance of ARGs (303 ARG subtypes, 197,816 x/Gb) compared to treated wastewater effluent (n = 2, 58 ARG subtypes, 2,692 x/Gb) and surface water (n = 5, 35 subtypes, 7,985 x/Gb). A cluster analysis showed that the taxonomic composition of wastewaters was highly similar and had a bacterial community composition enriched in gut bacteria (Bacteroides, Faecalibacterium, Bifidobacterium, Blautia, Roseburia, Ruminococcus), the Enterobacteriaceae group (Klebsiella, Aeromonas, Enterobacter) and opportunistic pathogens (Prevotella, Comamonas, Neisseria). Wastewater, treated effluents and surface waters had a shared resistome of 21 ARGs encoding multidrug resistant efflux pumps or resistance to aminoglycoside, macrolide-lincosamide-streptogramins (MLS), quinolones, sulfonamide, and tetracycline resistance which suggests that these genes are wide spread across different environments. Wastewater had a distinctively higher average abundance of clinically relevant, class A beta-lactamase resistant genes (i.e., blaKPC, blaCTX-M, blaSHV, blaTEM). The wastewaters from clinical isolation wards, in particular, had a exceedingly high levels of blaKPC-2 genes (142,200 x/Gb), encoding for carbapenem resistance. Assembled scaffolds (16 and 30 kbp) from isolation ward wastewater samples indicated this gene was located on a Tn3-based transposon (Tn4401), a mobilization element found in Klebsiella pneumonia plasmids. In the longer scaffold, transposable elements were flanked by a toxin–antitoxin (TA) system and other metal resistant genes that likely increase the persistence, fitness and propagation of the plasmid in the bacterial host under conditions of stress. A few bacterial species (Enterobacter cloacae, Klebsiella pneumoniae, Citrobacter freundii, Pseudomonas aeruginosa) that were cultured from the isolation ward wastewaters on CHROMagar media harbored the blaKPC-2 gene. This suggests that hospital wastewaters derived from clinical specialty wards are hotspots for the spread of AMR. Assembled scaffolds of other mobile genetic elements such as IncQ and IncF plasmids bearing quinolone resistance genes (qnrS1, qnrS2) and the class A beta-lactamase gene (blaTEM-1) were recovered in wastewater samples which may aid the transfer of AMR.
- Published
- 2017
- Full Text
- View/download PDF
7. Quantitative Detection of Active Vibrios Associated with White Plague Disease in Mussismilia braziliensis Corals
- Author
-
Luciane A. Chimetto Tonon, Janelle R. Thompson, Ana P. B. Moreira, Gizele D. Garcia, Kevin Penn, Rachelle Lim, Roberto G. S. Berlinck, Cristiane C. Thompson, and Fabiano L. Thompson
- Subjects
Vibrio coralliilyticus ,Mussismilia braziliensis ,pyrH gene ,reef health monitoring ,marine biology ,biodiversity ,Microbiology ,QR1-502 - Abstract
Over recent decades several coral diseases have been reported as a significant threat to coral reef ecosystems causing the decline of corals cover and diversity around the world. The development of techniques that improve the ability to detect and quantify microbial agents involved in coral disease will aid in the elucidation of disease cause, facilitating coral disease detection and diagnosis, identification and pathogen monitoring, pathogen sources, vectors, and reservoirs. The genus Vibrio is known to harbor pathogenic strains to marine organisms. One of the best-characterized coral pathogens is Vibrio coralliilyticus, an aetilogic agent of White Plague Disease (WPD). We used Mussismilia coral tissue (healthy and diseased specimens) to develop a rapid reproducible detection system for vibrios based on RT-QPCR and SYBR chemistry. We were able to detect total vibrios in expressed RNA targeting the 16S rRNA gene at 5.23 × 106 copies/μg RNA and V. coralliilyticus targeting the pyrH gene at 5.10 × 103 copies/μg RNA in coral tissue. Detection of V. coralliilyticus in diseased and in healthy samples suggests that WPD in the Abrolhos Bank may be caused by a consortium of microorganism and not only a single pathogen. We developed a more practical and economic system compared with probe uses for the real-time detection and quantification of vibrios from coral tissues by using the 16S rRNA and pyrH gene. This qPCR assay is a reliable tool for the monitoring of coral pathogens, and can be useful to prevent, control, or reduce impacts in this ecosystem.
- Published
- 2017
- Full Text
- View/download PDF
8. Correction: Sigma E Regulators Control Hemolytic Activity and Virulence in a Shrimp Pathogenic.
- Author
-
Pimonsri Rattanama, Janelle R. Thompson, Natthawan Kongkerd, Kanchana Srinitiwarawong, Varaporn Vuddhakul, and John J. Mekalanos
- Subjects
Medicine ,Science - Published
- 2012
- Full Text
- View/download PDF
9. A world of wastewater-based epidemiology
- Author
-
Andrew C. Singer, Janelle R. Thompson, César R. Mota Filho, Renée Street, Xiqing Li, Sara Castiglioni, and Kevin V. Thomas
- Published
- 2023
10. Co-incidence of BA.1 and BA.2 at the start of Singapore's Omicron wave revealed by community and university campus wastewater surveillance
- Author
-
Feng Jun Desmond Chua, Se Yeon Kim, Eric Hill, Jia Wei Cai, Wei Lin Lee, Xiaoqiong Gu, Siti Aisyah Afri Affandi, Wee Chiew Germaine Kwok, Weijie Ng, Mats Leifels, Federica Armas, Franciscus Chandra, Hongjie Chen, Eric J. Alm, Martin Tay, Chui Ching Judith Wong, Lee Ching Ng, Stefan Wuertz, Janelle R. Thompson, School of Biological Sciences, Asian School of the Environment, School of Civil and Environmental Engineering, National Environmental Agency, Campus for Research Excellence and Technological Enterprise (CREATE), and Singapore Centre for Environmental Life Sciences and Engineering (SCELSE)
- Subjects
Bioengineering [Engineering] ,Environmental Engineering ,SARS-CoV-2 ,Environmental Chemistry ,COVID-19 ,Pollution ,Waste Management and Disposal - Abstract
Wastewater surveillance (WWS) has been globally recognised to be a useful tool in quantifying SARS-CoV-2 RNA at the community and residential levels without biases associated with case-reporting. The emergence of variants of concern (VOCs) have given rise to an unprecedented number of infections even though populations are increasingly vaccinated. This is because VOCs have been reported to possess higher transmissibility and can evade host immune responses. The B.1.1.529 lineage (Omicron) has severely disrupted global plans to return to normalcy. In this study, we developed an allele-specific (AS) RT-qPCR assay which simultaneously targets the stretch of deletions and mutations in the spike protein from position 24-27 for quantitative detection of Omicron BA.2. Together with previous assays that detect mutations associated with Omicron BA.1 (deletion at position 69 and 70) and all Omicron (mutation at position 493 and 498), we report the validation and time series of these assays from September 2021 to May 2022 using influent samples from two wastewater treatment plants and across four University campus sites in Singapore. Viral RNA concentrations at the treatment plants corroborate with locally reported clinical cases, AS RT-qPCR assays revealed co-incidence of Omicron BA.1 and BA.2 on 12 January 2022, almost two months after initial BA.1 detection in South Africa and Botswana. BA.2 became the dominant variant by the end of January 2022 and completely displaced BA.1 by mid-March 2022. University campus sites were similarly positive for BA.1 and/or BA.2 in the same week as first detection at the treatment plants, where BA.2 became rapidly established as the dominant lineage within three weeks. These results corroborate clinical incidence of the Omicron lineages in Singapore and indicate minimal silent circulation prior to January 2022. The subsequent simultaneous spread of both variant lineages followed strategic relaxation of safe management measures upon meeting nationwide vaccination goals. Ministry of Education (MOE) National Environmental Agency (NEA) National Research Foundation (NRF) Published version This research is supported by the National Research Foundation, Prime Minister's Office, Singapore, under its Campus for Research Excellence and Technological Enterprise (CREATE) program funding to the Singapore Centre for Environmental Life Sciences Engineering (SCELSE) and the IntraCREATE Thematic Grant (Cities) grant NRF2019-THE001-0003a to SW & JT, the National Environmental Agency (NEA) of Singapore, and funding from the Singapore Ministry of Education and National Research Foundation through an RCE award to SCELSE.
- Published
- 2023
11. Persistence of Dengue (Serotypes 2 and 3), Zika, Yellow Fever, and Murine Hepatitis Virus RNA in Untreated Wastewater
- Author
-
Hongjie Chen, Wei Lin Lee, Mats Leifels, Stefan Wuertz, Eric J. Alm, Franciscus Chandra, Federica Armas, Janelle R. Thompson, Xiaoqiong Gu, School of Chemical and Biomedical Engineering, Asian School of the Environment, Campus for Research Excellence and Technological Enterprise (CREATE), and Singapore Centre for Environmental Life Sciences and Engineering (SCELSE)
- Subjects
Serotype ,Murine hepatitis ,Ecology ,Health, Toxicology and Mutagenesis ,Yellow fever ,RNA ,Untreated wastewater ,Freeze-Thaw ,Biology ,medicine.disease ,Pollution ,Virology ,Virus ,Environmental engineering [Engineering] ,Persistence (computer science) ,Dengue fever ,Cyclesclimate-Change ,medicine ,Environmental Chemistry ,Waste Management and Disposal ,Water Science and Technology - Abstract
Arboviruses are viral pathogens transmitted by blood-borne vectors that impose a great social and economic burden globally. Most clinical surveillance of arbovirus outbreaks underestimates the true prevalence as a large proportion of cases exhibit no or only mild clinical symptoms (i.e., are subclinical). Reports of urinary shedding of several arboviruses such as Dengue (DENV), yellow fever (YFV), and Zika (ZIKV) viruses suggest the possibility of utilizing wastewater surveillance to assess the prevalence of arboviral outbreaks. To determine the feasibility of wastewater surveillance, we investigated the decay of representative arboviruses (including DENV-2, DENV-3, YFV, and ZIKV) along with murine hepatitis virus (MHV) as a surrogate for human coronavirus within a wastewater matrix at 6, 25, or 37 °C using RT-qPCR. DENV-2, DENV-3, YFV, ZIKV, and MHV experienced a one log10reduction within 3.95-6.21 days at 25 °C and within 2.60-5.12 days at 37 °C, while incubation at 6 °C did not indicate substantial decay within 21 days. Our work suggests that these arboviruses or their RNA could persist sufficiently in wastewater over a range of temperatures, supporting the potential for wastewater-based surveillance of arboviral outbreaks. Ministry of Education (MOE) National Research Foundation (NRF) Singapore-MIT Alliance for Research and Technology (SMART) This research was supported by the National Research Foundation, Prime Minister’s Office, Singapore, under its Campus for Research Excellence and Technological Enterprise (CREATE) program, through Intra-CREATE Thematic Grant (Cities) Grant NRF2019-THE001-0003 to J.T. and E.J.A., the Singapore-MIT Alliance for Research and Technology (SMART) Antimicrobial Resistance Interdisciplinary Research Group (AMR IRG), and funding from the Singapore Ministry of Education and National Research Foundation through an RCE award to the Singapore Centre for Environmental Life Sciences Engineering (SCELSE).
- Published
- 2021
12. Coral mucus rapidly induces chemokinesis and genome-wide transcriptional shifts toward early pathogenesis in a bacterial coral pathogen
- Author
-
Jean-Baptiste Raina, Vicente I. Fernandez, Janelle R. Thompson, Cherry Gao, Melissa Garren, Justin R. Seymour, Roman Stocker, and Kevin Penn
- Subjects
Coral ,Chemokinesis ,Video microscopy ,Biology ,Bacterial pathogenesis ,marine microbiology ,microbial ecology ,Microbiology ,Article ,Microbial ecology ,Downregulation and upregulation ,Marine microbiology ,Animals ,Seawater ,Ecology, Evolution, Behavior and Systematics ,Vibrio ,Virulence ,Vibrio coralliilyticus ,Chemotaxis ,fungi ,technology, industry, and agriculture ,biochemical phenomena, metabolism, and nutrition ,biology.organism_classification ,Anthozoa ,Mucus ,Quorum sensing ,05 Environmental Sciences, 06 Biological Sciences, 10 Technology - Abstract
Elevated seawater temperatures have contributed to the rise of coral disease mediated by bacterial pathogens, such as the globally distributed Vibrio coralliilyticus, which utilizes coral mucus as a chemical cue to locate stressed corals. However, the physiological events in the pathogens that follow their entry into the coral host environment remain unknown. Here, we present simultaneous measurements of the behavioral and transcriptional responses of V. coralliilyticus BAA-450 incubated in coral mucus. Video microscopy revealed a strong and rapid chemokinetic behavioral response by the pathogen, characterized by a two-fold increase in average swimming speed within 6 min of coral mucus exposure. RNA sequencing showed that this bacterial behavior was accompanied by an equally rapid differential expression of 53% of the genes in the V. coralliilyticus genome. Specifically, transcript abundance 10 min after mucus exposure showed upregulation of genes involved in quorum sensing, biofilm formation, and nutrient metabolism, and downregulation of flagella synthesis and chemotaxis genes. After 60 min, we observed upregulation of genes associated with virulence, including zinc metalloproteases responsible for causing coral tissue damage and algal symbiont photoinactivation, and secretion systems that may export toxins. Together, our results suggest that V. coralliilyticus employs a suite of behavioral and transcriptional responses to rapidly shift into a distinct infection mode within minutes of exposure to the coral microenvironment., The ISME Journal, 15 (12), ISSN:1751-7362, ISSN:1751-7370
- Published
- 2021
13. Mussismilia braziliensis White Plague Disease Is Characterized by an Affected Coral Immune System and Dysbiosis
- Author
-
C. Thompson, Carlos Alberto Nunes Cosenza, Fabiano L. Thompson, Janelle R. Thompson, Jean Swings, Mónica Medina, Kevin Penn, L A C Tonon, G D Garcia, Adriana M. Fróes, and Arthur W. Silva-Lima
- Subjects
0301 basic medicine ,Ecology ,biology ,030106 microbiology ,Pantoea ,Soil Science ,medicine.disease ,biology.organism_classification ,Microbiology ,Transcriptome ,Intracellular signal transduction ,03 medical and health sciences ,030104 developmental biology ,Microbial ecology ,Gammaproteobacteria ,medicine ,Dysbiosis ,Ecology, Evolution, Behavior and Systematics ,Bacteria ,Symbiotic bacteria - Abstract
Infectious diseases are one of the major drivers of coral reef decline worldwide. White plague-like disease (WPL) is a widespread disease with a complex etiology that infects several coral species, including the Brazilian endemic species Mussismilia braziliensis. Gene expression profiles of healthy and WPL-affected M. braziliensis were analyzed in winter and summer seasons. The de novo assembly of the M. braziliensis transcriptome from healthy and white plague samples produced a reference transcriptome containing 119,088 transcripts. WPL-diseased samples were characterized by repression of immune system and cellular defense processes. Autophagy and cellular adhesion transcripts were also repressed in WPL samples, suggesting exhaustion of the coral host defenses. Seasonal variation leads to plasticity in transcription with upregulation of intracellular signal transduction, apoptosis regulation, and oocyte development in the summer. Analysis of the active bacterial rRNA indicated that Pantoea bacteria were more abundant in WPL corals, while Tistlia, Fulvivirga, and Gammaproteobacteria Ga0077536 were more abundant in healthy samples. Cyanobacteria proliferation was also observed in WPL, mostly in the winter. These results indicate a scenario of dysbiosis in WPL-affected M. braziliensis, with the loss of potentially symbiotic bacteria and proliferation of opportunistic microbes after the start of the infection process.
- Published
- 2020
14. Insights on the genetic repertoire of the coral Mussismilia braziliensis endosymbiont Symbiodinium
- Author
-
Tooba Varasteh, Arthur Weiss da Silva Lima, Mónica Medina, Luciana Leomil, Cristiane C. Thompson, Fabiano L. Thompson, Louisi de Oliveira, and Janelle R. Thompson
- Subjects
0106 biological sciences ,0301 basic medicine ,Coral bleaching ,Cytochrome P450 ,Biology ,biology.organism_classification ,01 natural sciences ,Cell biology ,Transcriptome ,03 medical and health sciences ,Symbiodinium ,030104 developmental biology ,Prophase ,Symbiosis ,biology.protein ,General Agricultural and Biological Sciences ,Developmental biology ,Mitosis ,010606 plant biology & botany - Abstract
Reef-building corals form a symbiotic association with photosynthetic dinoflagellates of the family Symbiodiniaceae. This symbiosis is crucial for the maintenance of coral reefs. In this work, we evaluate the effect of light conditions on the transcriptomic response of Symbiodinium CCMR0100 (ITS2 type A4), isolated from the Southwestern Atlantic Ocean endemic Mussismilia braziliensis. We obtained a total of 36,224 transcripts (N50 = 1007 bases, mean GC = 55.7%; ~25 Gb of assembled bases). We observed ecologically relevant transcripts encoding i. the complete antioxidant enzymatic system, ii. the recently described algal dimethylsulfoniopropionate (DMSP) lyase, and iii. The Mycosporine-like aminoacids (MAA) biosynthesis pathway. Cultures maintained in dark and light conditions yielded different transcriptomic profiles, and 48 transcripts were differentially expressed between these treatments. Expression of cytochrome P450 was inhibited by light, suggesting that endoplasmic reticulum monooxygenase activity might play a role in light-independent coral bleaching. Light conditions also triggered the induction of transcripts associated to chromatin condensation and mitosis, consistent with the light dependent progression of Symbiodiniaceae cell cycle. The repression of transcripts associated to the phosphatidylinositol (PI) signaling pathwaysuggests this pathway shall be related to light-induced morphological changes in Symbiodiniaceae cell.
- Published
- 2020
15. Low Gut Ruminococcaceae Levels are Associated with Occurrence of Antibiotic-associated Diarrhea
- Author
-
Shijie Zhao, Hongjie Chen, Wei Lin Lee, Zhanyi Lee, Federica Armas, Shirin Kalimuddin, Eric J. Alm, Yvonne Fz Chan, Ega Danu Chang, Xiaoqiong Gu, Janelle R. Thompson, Liang Cui, Eng Eong Ooi, Jenny G. Low, An-Ni Zhang, Franciscus Chandra, Yii Ean Teh, and Jean Xy Sim
- Subjects
medicine.medical_specialty ,biology ,medicine.drug_class ,business.industry ,Antibiotics ,Faecalibacterium prausnitzii ,biology.organism_classification ,Discontinuation ,Diarrhea ,Internal medicine ,medicine ,Microbiome ,medicine.symptom ,Antibiotic-associated diarrhea ,business ,Adverse effect ,Ruminococcaceae - Abstract
Patients receiving antibiotics often suffer from antibiotic-associated diarrhea (AAD). AAD is of clinical significance as it can result in premature antibiotic discontinuation and suboptimal treatment of infection. The drivers of AAD however, remain poorly understood. We sought to understand if differences in the gut microbiome, both at baseline and during antibiotic administration, would influence the development of AAD. We administered a 3-day course of oral amoxicillin-clavulanate to 30 healthy adult volunteers, and performed a detailed interrogation of their stool microbiome at baseline and up to 4-weeks post antibiotic administration, using 16S rRNA gene sequencing. Lower levels of Ruminococcaceae were significantly and consistently observed from baseline till Day 7 in participants who developed AAD. The probability of AAD could be predicted based on qPCR-derived levels of Faecalibacterium prausnitzii, the most dominant species within the Ruminococcaceae family. Overall, participants who developed AAD experienced a greater decrease in microbial diversity during antibiotic dosing. Our findings suggest that a lack of gut Ruminococcaceae at baseline influences development of AAD. In addition, quantification of F. prausnitzii in stool prior to antibiotic administration may help identify patients at risk of AAD, and aid clinicians in devising individualised treatment regimens to minimise such adverse effects.
- Published
- 2021
16. Quantitative SARS-CoV-2 tracking of variants Delta, Delta plus, Kappa and Beta in wastewater by allele-specific RT-qPCR
- Author
-
Fuqing Wu, Federica Armas, Eric J. Alm, Franciscus Chandra, Claire Y. J. Lim, Xiaoqiong Gu, Amy Xiao, Mats Leifels, Shrestha Jolly, Feng Jun Desmond Chua, Janelle R. Thompson, Hongjie Chen, Wei Lin Lee, and Germaine Wc Kwok
- Subjects
Delta ,2019-20 coronavirus outbreak ,Coronavirus disease 2019 (COVID-19) ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Design elements and principles ,Biology ,Beta (finance) ,Virology ,Allele specific ,Kappa - Abstract
The Delta (B.1.617.2) variant has caused major devastation in India and other countries around the world. First detected in October 2020, it has now spread to more than 100 countries, prompting WHO to declare it as a global variant of concern (VOC). The Delta (B.1.617.2), Delta plus (B.1.617.2.1) and Kappa (B.1.617.1) variants are all sub-lineages of the original B.1.617 variant. Prior to the inception of B.1.617, vaccine rollout, safe-distancing and timely lockdowns greatly reduced COVID-19 hospitalizations and deaths. However, the Delta variant, allegedly more infectious and for which existing vaccines seemed less effective, has catalyzed the resurgence of cases. Therefore, there is an imperative need for increased surveillance of the B.1.617 variants. While the Beta variant is increasingly outpaced by the Delta variant, the spread of the Beta variant remains of concern due to its vaccine resistance. Efforts have been made to utilize wastewater-based surveillance for community-based tracking of SARS-CoV-2 variants, however wastewater with its low SARS-CoV-2 viral titers and mixtures of viral variants, requires assays to be variant-specific yet accurately quantitative for meaningful interpretation. Following on the design principles of our previous assays for the Alpha variant, here we report allele-specific and multiplex-compatible RT-qPCR assays targeting mutations T19R, D80A, K417N, T478K and E484Q, for quantitative detection and discrimination of the Delta, Delta plus, Kappa and Beta variants in wastewater. This method is open-sourced and can be implemented using commercially available RT-qPCR protocols, and would be an important tool for tracking the spread of B.1.617 and the Beta variants in communities.
- Published
- 2021
17. Minimizing Errors in RT-PCR Detection and Quantification of SARS-CoV-2 RNA for Wastewater Surveillance
- Author
-
Tarja Pitkänen, Rosalie Subburg, Albert Bosch, Coleen C. Naughton, Kyle Bibby, Kerry A. Hamilton, Marta Rusiñol, Joan B. Rose, Wendy Smith, Andrew S. Whiteley, Charles N. Haas, Irene Xagoraraki, Valerie J. Harwood, Heather M. Murphy, Giuseppina La Rosa, Qian Zhang, Michael J. Sadowsky, Sandra L. McLellan, Asja Korajkic, Brandon Reyneke, Kevin V. Thomas, Sílvia Bofill-Mas, Susan Petterson, Daniel Gerrity, Hapuarachchige Chanditha Hapuarachchi, Verónica Beatriz Rajal, Rehnuma Haque, Suzanne Metcalfe, Simon Toze, Paul M. Bertsch, Yin Xiang Setoh, Rachel T. Noble, Daisuke Sano, Andreas H. Farnleitner, Nishita D'Souza, John F. Griffith, Phong K. Thai, Wesaal Khan, Warish Ahmed, Brian R. McMinn, Stefan Wuertz, Josh Tynan, Aaron Bivins, Linda L. Blackall, Orin C. Shanks, Fernando A. Roman, João Brandão, Amity G. Zimmer-Faust, Mark Ciesielski, Samendra P. Sherchan, Raul Gonzalez, Judith Chui Ching Wong, Stuart L. Simpson, Erin K. Lipp, Janelle R. Thompson, Erica Donner, Jochen F. Mueller, Laura Sala-Comorera, Blythe A. Layton, Joshua A. Steele, Gertjan Medema, Greg Jackson, Phil M. Choi, Erin M. Symonds, Wim G. Meijer, Stuart J. Khan, Masaaki Kitajima, Sudhi Payyappat, Kwanrawee Sirikanchana, Pradip Gyawali, Ahmed, Warish, Simpson, Stuart L, Bertsch, Paul M, Bibby, Kyle, Donner, Erica, Shanks, Orin C, Bosch, Albert, Brandão, Joao, La Rosa, Giuseppina, McLellan, Sandra L., Noble, Rachel T., Bosch, Albert [0000-0002-8111-9059], Brandão, Joao [0000-0001-7553-227X], La Rosa, Giuseppina [0000-0002-2657-100X], McLellan, Sandra L. [0000-0003-3283-1151], and Noble, Rachel T. [0000-0001-9071-8312]
- Subjects
False negative ,Epidemiology ,0211 other engineering and technologies ,02 engineering and technology ,Review ,Wastewater ,010501 environmental sciences ,01 natural sciences ,Aigües residuals ,Pandemic ,Digital polymerase chain reaction ,Prospective Studies ,False positive ,Waste Management and Disposal ,0303 health sciences ,Surveillance ,Warning system ,Sewage ,Reverse Transcriptase Polymerase Chain Reaction ,false negative ,Pollution ,6. Clean water ,3. Good health ,Real-time polymerase chain reaction ,RNA, Viral ,False-negative ,Wastewater-Based Epidemiological Monitoring ,false positive ,medicine.medical_specialty ,Environmental Engineering ,Coronavirus disease 2019 (COVID-19) ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,RT-PCR ,03 medical and health sciences ,False-positive ,medicine ,Humans ,Environmental Chemistry ,Intensive care medicine ,Epidemiologia ,Pandemics ,Retrospective Studies ,030304 developmental biology ,0105 earth and related environmental sciences ,021110 strategic, defence & security studies ,business.industry ,SARS-CoV-2 ,other ,RNA ,Reproducibility of Results ,Data interpretation ,COVID-19 ,Virology ,Environmental science ,business ,Quality assurance - Abstract
Wastewater surveillance for pathogens using reverse transcription-polymerase chain reaction (RT-PCR) is an effective and resource-efficient tool for gathering community-level public health information, including the incidence of coronavirus disease-19 (COVID-19). Surveillance of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in wastewater can potentially provide an early warning signal of COVID-19 infections in a community. The capacity of the world's environmental microbiology and virology laboratories for SARS-CoV-2 RNA characterization in wastewater is increasing rapidly. However, there are no standardized protocols or harmonized quality assurance and quality control (QA/QC) procedures for SARS-CoV-2 wastewater surveillance. This paper is a technical review of factors that can cause false-positive and false-negative errors in the surveillance of SARS-CoV-2 RNA in wastewater, culminating in recommended strategies that can be implemented to identify and mitigate some of these errors. Recommendations include stringent QA/QC measures, representative sampling approaches, effective virus concentration and efficient RNA extraction, PCR inhibition assessment, inclusion of sample processing controls, and considerations for RT-PCR assay selection and data interpretation. Clear data interpretation guidelines (e.g., determination of positive and negative samples) are critical, particularly when the incidence of SARS-CoV-2 in wastewater is low. Corrective and confirmatory actions must be in place for inconclusive results or results diverging from current trends (e.g., initial onset or reemergence of COVID-19 in a community). It is also prudent to perform interlaboratory comparisons to ensure results' reliability and interpretability for prospective and retrospective analyses. The strategies that are recommended in this review aim to improve SARS-CoV-2 characterization and detection for wastewater surveillance applications. A silver lining of the COVID-19 pandemic is that the efficacy of wastewater surveillance continues to be demonstrated during this global crisis. In the future, wastewater should also play an important role in the surveillance of a range of other communicable diseases.
- Published
- 2021
18. Temporal trends of perfluoroalkyl substances in an Australian wastewater treatment plant: A ten-year retrospective investigation
- Author
-
Timothy Reeks, Jennifer Braeunig, Christie Gallen, G. Taucare, Janelle R. Thompson, Anders Bignert, Jake W. O'Brien, and Jochen F. Mueller
- Subjects
education.field_of_study ,Fluorocarbons ,Environmental Engineering ,Population ,Australia ,Wastewater ,Pollution ,Water Purification ,Australian population ,Alkanesulfonic Acids ,Environmental health ,Environmental Chemistry ,Environmental science ,Sewage treatment ,education ,Waste Management and Disposal ,Retrospective Studies - Abstract
Per- and poly-fluoroalkyl substances (PFAS) are a problematic group of chemicals used in various industrial and household products. They have been extensively detected in wastewater as a result of day-to-day product usage. Due to concerns about their safety, voluntary and regulatory action to limit the manufacture and use of some individual PFAS has occurred since the year 2000. The impact that this intervention has had on the use and potential exposure of Australians has not been measured. Wastewater serves as a powerful tool to assess the chemical use or consumption patterns of a population over time. We accessed a ten-year wastewater archiving program to conduct a temporal analysis of PFAS trends in an urban Australian population between the years 2010 and 2020. Results showed a decline in the concentrations for most PFAS, and a change in the PFAS profile from perfluorosulfonic acids and long-chain perfluorocarboxylic acids, to the short-chain perfluorocarboxylic acids and PFOS-replacement degradation products such as 5:3 FTCA. Intermittent pulses of PFAS that were significantly higher than ‘background’ levels (i.e., representing the PFAS input from primarily households) were observed, suggesting continuing industrial PFAS input within the wastewater catchment. This study highlights the long-term consequences of the diffuse use of persistent chemicals in products, and their ability to continue to enter the wastewater stream for decades.
- Published
- 2021
19. Quantitative detection of SARS-CoV-2 B.1.1.7 variant in wastewater by allele-specific RT-qPCR
- Author
-
Fuqing Wu, Xiaoqiong Gu, Shane T. Wilson, Eric J. Alm, Roisin Sullivan, Amy Xiao, Kyle A. McElroy, Janelle R. Thompson, Samuel Mendola, Federica Armas, Maxim Imakaev, Morgan M. Powell, Hongjie Chen, Wei Lin Lee, Claire Duvallet, Mariana Matus, Katya Moniz, Mats Leifels, Franciscus Chandra, and Newsha Ghaeli
- Subjects
2019-20 coronavirus outbreak ,Coronavirus disease 2019 (COVID-19) ,Wastewater ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Genomic sequencing ,Spike Protein ,Computational biology ,Biology ,Allele specific - Abstract
Wastewater-based epidemiology (WBE) has emerged as a critical public health tool in tracking the SARS-CoV-2 epidemic. Monitoring SARS-CoV-2 variants of concern in wastewater has to-date relied on genomic sequencing, which lacks sensitivity necessary to detect low variant abundances in diluted and mixed wastewater samples. Here, we develop and present an open-source method based on allele specific RT-qPCR (AS RT-qPCR) that detects and quantifies the B.1.1.7 variant, targeting spike protein mutations at three independent genomic loci highly predictive of B.1.1.7 (HV69/70del, Y144del, and A570D). Our assays can reliably detect and quantify low levels of B.1.1.7 with low cross-reactivity, and at variant proportions between 0.1% and 1% in a background of mixed SARS-CoV-2. Applying our method to wastewater samples from the United States, we track B.1.1.7 occurrence over time in 19 communities. AS RT-qPCR results align with clinical trends, and summation of B.1.1.7 and wild-type sequences quantified by our assays strongly correlate with SARS-CoV-2 levels indicated by the US CDC N1/N2 assay. This work paves the path for rapid inexpensive surveillance of B.1.1.7 and other SARS-CoV-2 variants in wastewater.
- Published
- 2021
20. Wastewater Surveillance of SARS-CoV-2 across 40 U.S. states
- Author
-
Newsha Ghaeli, Mariana Matus, Xiaoqiong Gu, Steven F Rhode, Eric J. Alm, Fuqing Wu, Janelle R. Thompson, Amy Xiao, Katya Moniz, Mary Bushman, William P. Hanage, Katherine H. Huang, Kyle A. McElroy, Katelyn Foppe, Noriko Endo, Wei Lin Lee, Claire Duvallet, Stefan Wuertz, Jianbo Zhang, Peter R. Chai, Timothy B. Erickson, and Federica Armas
- Subjects
education.field_of_study ,Disease surveillance ,Coronavirus disease 2019 (COVID-19) ,SARS-CoV-2 ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Incidence (epidemiology) ,Population ,Outbreak ,COVID-19 ,Wastewater ,Article ,Disease Outbreaks ,Environmental health ,Environmental science ,Humans ,RNA, Viral ,Sewage treatment ,education - Abstract
Wastewater-based disease surveillance is a promising approach for monitoring community outbreaks. Here we describe a nationwide campaign to monitor SARS-CoV-2 in the wastewater of 159 counties in 40 U.S. states, covering 13% of the U.S. population from February 18 to June 2, 2020. Out of 1,751 total samples analyzed, 846 samples were positive for SARS-CoV-2 RNA, with overall viral concentrations declining from April to May. Wastewater viral titers were consistent with, and appeared to precede, clinical COVID-19 surveillance indicators, including daily new cases. Wastewater surveillance had a high detection rate (>80%) of SARS-CoV-2 when the daily incidence exceeded 13 per 100,000 people. Detection rates were positively associated with wastewater treatment plant catchment size. To our knowledge, this work represents the largest-scale wastewater-based SARS-CoV-2 monitoring campaign to date, encompassing a wide diversity of wastewater treatment facilities and geographic locations. Our findings demonstrate that a national wastewater-based approach to disease surveillance may be feasible and effective.
- Published
- 2021
21. Gut Ruminococcaceae Levels Correlate with Risk of Antibiotic-Associated Diarrhea
- Author
-
Xiaoqiong Gu, Jean XY Sim, Wei Lin Lee, Yvonne FZ Chan, Ega Danu Chang, Yii Ean Teh, An-Ni Zhang, Federica Armas, Franciscus Chandra, Chen Hongjie, shijie zhao, Zhanyi Lee, Janelle R. Thompson, Eng Eong Ooi, Jenny G. Low, Eric J. Alm, and Shirin Kalimuddin
- Subjects
History ,Polymers and Plastics ,Business and International Management ,Industrial and Manufacturing Engineering - Published
- 2021
22. Quantitative SARS-CoV-2 alpha variant B.1.1.7 tracking in wastewater by allele-specific RT-qPCR
- Author
-
Newsha Ghaeli, Shane T. Wilson, Hongjie Chen, Wei Lin Lee, Claire Duvallet, Mariana Matus, Róisín Floyd-O’Sullivan, Franciscus Chandra, Mats Leifels, Janelle R. Thompson, Katya Moniz, Amy Xiao, Eric J. Alm, Federica Armas, Samuel Mendola, Claire Y. J. Lim, Maxim Imakaev, Morgan M. Powell, Fuqing Wu, Karl L. J. Berge, Kyle A. McElroy, Xiaoqiong Gu, Asian School of the Environment, Campus for Research Excellence and Technological Enterprise (CREATE), Singapore Centre for Environmental Life Sciences and Engineering (SCELSE), Massachusetts Institute of Technology. Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology. Department of Biological Engineering, and Singapore-MIT Alliance in Research and Technology (SMART)
- Subjects
2019-20 coronavirus outbreak ,Ecology ,Coronavirus disease 2019 (COVID-19) ,Health, Toxicology and Mutagenesis ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Alpha (ethology) ,Spike Protein ,Amplification ,Computational biology ,DNA ,Biology ,Pollution ,Chemical society ,Environmental engineering [Engineering] ,Wastewater ,Environmental Chemistry ,Waste Management and Disposal ,Allele specific ,Water Science and Technology - Abstract
The critical need for surveillance of SARS-CoV-2 variants of concern has prompted the development of methods that can track variants in wastewater. Here, we develop and present an open-source method based on allele-specific RT-qPCR (AS RT-qPCR) that detects and quantifies the B.1.1.7 variant, targeting spike protein mutations at three independent genomic loci that are highly predictive of B.1.1.7 (HV69/70del, Y144del, and A570D). Our assays can reliably detect and quantify low levels of B.1.1.7 with low cross-reactivity, and at variant proportions down to 1% in a background of mixed SARS-CoV-2. Applying our method to wastewater samples from the United States, we track the occurrence of B.1.1.7 over time in 19 communities. AS RT-qPCR results align with clinical trends, and summation of B.1.1.7 and wild-Type sequences quantified by our assays matches SARS-CoV-2 levels indicated by the U.S. CDC N1 and N2 assays. This work paves the way for AS RT-qPCR as a method for rapid inexpensive surveillance of SARS-CoV-2 variants in wastewater. Ministry of Education (MOE) National Research Foundation (NRF) Published version This research is supported by the National Research Foundation, Prime Minister's Office, Singapore, under its Campus for Research Excellence and Technological Enterprise (CREATE) program, Intra-CREATE Thematic Grant (Cities) Grant NRF2019-THE001-0003a to J.T. and E. J.A., and funding from the Singapore Ministry of Education and National Research Foundation through an RCE award to the Singapore Centre for Environmental Life Sciences Engineering (SCELSE) to J.T. This work was also supported by funds from the Massachusetts Consortium on Pathogen Readiness and China Evergrande Group (M.M. and E.J.A.).
- Published
- 2021
23. Gut Ruminococcaceae Levels Correlate with Risk of Antibiotic-Associated Diarrhea
- Author
-
Franciscus Chandra, Jean Xy Sim, Liang Cui, Janelle R. Thompson, Xiaoqiong Gu, Chen Hongjie, Jenny G. Low, An-Ni Zhang, Federica Armas, Shijie Zhao, Zhanyi Lee, Yvonne Fz Chan, Eng Eong Ooi, Ega Danu Chang, Wei Lin Lee, Yii Ean Teh, Eric J. Alm, and Shirin Kalimuddin
- Subjects
History ,medicine.medical_specialty ,Polymers and Plastics ,biology ,business.industry ,medicine.drug_class ,Antibiotics ,Faecalibacterium prausnitzii ,biology.organism_classification ,Industrial and Manufacturing Engineering ,Gut microbiome ,Diarrhea ,Internal medicine ,medicine ,Microbiome ,Business and International Management ,medicine.symptom ,Antibiotic-associated diarrhea ,Adverse effect ,business ,Ruminococcaceae - Abstract
Antibiotic-associated diarrhea (AAD) affects a significant proportion of patients receiving antibiotics. We sought to understand if differences in the gut microbiome would influence the development of AAD. We administered a 3-day course of amoxicillin-clavulanate to 30 healthy adult volunteers, and analyzed their stool microbiome, using 16S rRNA gene sequencing, at baseline and up to 4-weeks post-antibiotic administration. Lower levels of gut Ruminococcaceae were significantly and consistently observed from baseline till Day 7 in participants who developed AAD. Overall, participants who developed AAD experienced a greater decrease in microbial diversity. The probability of AAD could be predicted based on qPCR-derived levels of Faecalibacterium prausnitzii . Our findings suggest that a lack of gut Ruminococcaceae influences development of AAD. Quantification of F. prausnitzii in stool prior to antibiotic administration may help identify patients at risk of AAD, and aid clinicians in devising individualised treatment regimens to minimise such adverse effects.
- Published
- 2021
24. Metrics to relate COVID-19 wastewater data to clinical testing dynamics
- Author
-
William P. Hanage, Steven F Rhode, Timothy B. Erickson, Katya Moniz, Xiaoqiong Gu, Kyle A. McElroy, Federica Armas, Janelle R. Thompson, Claire Duvallet, Jianbo Zhang, Amy Xiao, Maxim Imakaev, Eric J. Alm, Mariana Matus, Hongjie Chen, Peter R. Chai, Wei Lin Lee, Brian J. Arnold, Franciscus Chandra, Newsha Ghaeli, Fuqing Wu, Mary Bushman, Noriko Endo, Asian School of the Environment, Campus for Research Excellence and Technological Enterprise (CREATE), Singapore, and Singapore Centre for Environmental Life Sciences and Engineering (SCELSE)
- Subjects
medicine.medical_specialty ,Wastewater-Based Epidemiological Monitoring ,Environmental Engineering ,Coronavirus disease 2019 (COVID-19) ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Wastewater-based epidemiology ,Context (language use) ,Wastewater Surveillance ,Wastewater ,Article ,Environmental health ,Pandemic ,Epidemiology ,medicine ,Humans ,Temporal dynamics ,Pandemics ,Waste Management and Disposal ,Water Science and Technology ,Civil and Structural Engineering ,SARS-CoV-2 ,Public health ,Ecological Modeling ,COVID-19 ,Pollution ,Environmental engineering [Engineering] ,Benchmarking ,Environmental science ,RNA, Viral ,Wastewater-Based Epidemiology ,Sewage treatment ,Wastewater surveillance - Abstract
Wastewater surveillance has emerged as a useful tool in the public health response to the COVID-19 pandemic. While wastewater surveillance has been applied at various scales to monitor population-level COVID-19 dynamics, there is a need for quantitative metrics to interpret wastewater data in the context of public health trends. 24-hour composite wastewater samples were collected from March 2020 through May 2021 from a Massachusetts wastewater treatment plant and SARS-CoV-2 RNA concentrations were measured using RT-qPCR. The relationship between wastewater copy numbers of SARS-CoV-2 gene fragments and COVID-19 clinical cases and deaths varies over time. We demonstrate the utility of three new metrics to monitor changes in COVID-19 epidemiology: (1) the ratio between wastewater copy numbers of SARS-CoV-2 gene fragments and clinical cases (WC ratio), (2) the time lag between wastewater and clinical reporting, and (3) a transfer function between the wastewater and clinical case curves. The WC ratio increases after key events, providing insight into the balance between disease spread and public health response. Time lag and transfer function analysis showed that wastewater data preceded clinically reported cases in the first wave of the pandemic but did not serve as a leading indicator in the second wave, likely due to increased testing capacity, which allows for more timely case detection and reporting. These three metrics could help further integrate wastewater surveillance into the public health response to the COVID-19 pandemic and future pandemics., Graphical abstract Image, graphical abstract
- Published
- 2022
25. SARS-CoV-2 Titers in Wastewater Are Higher than Expected from Clinically Confirmed Cases
- Author
-
Claire Duvallet, Katya Moniz, Alex D. Washburne, Mariana Matus, Jianbo Zhang, Newsha Ghaeli, Timothy B. Erickson, Kathryn M. Kauffman, Fuqing Wu, Wei Lin Lee, Noriko Endo, Peter R. Chai, William P. Hanage, Mathilde Poyet, Eric J. Alm, Xiaoqiong Gu, Amy Xiao, Federica Armas, and Janelle R. Thompson
- Subjects
0301 basic medicine ,medicine.medical_specialty ,Physiology ,030106 microbiology ,Population ,lcsh:QR1-502 ,Sewage ,Disease ,010501 environmental sciences ,01 natural sciences ,Biochemistry ,Microbiology ,lcsh:Microbiology ,03 medical and health sciences ,Environmental health ,Modelling and Simulation ,Case fatality rate ,Pandemic ,Epidemiology ,Genetics ,Medicine ,education ,viral titers ,wastewater ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,0105 earth and related environmental sciences ,education.field_of_study ,business.industry ,SARS-CoV-2 ,Outbreak ,COVID-19 prevalence ,QR1-502 ,Computer Science Applications ,Wastewater ,Modeling and Simulation ,PMMoV ,business - Abstract
Wastewater surveillance represents a complementary approach to clinical surveillance to measure the presence and prevalence of emerging infectious diseases like the novel coronavirus SARS-CoV-2. This innovative data source can improve the precision of epidemiological modeling to understand the penetrance of SARS-CoV-2 in specific vulnerable communities. Here, we tested wastewater collected at a major urban treatment facility in Massachusetts and detected SARS-CoV-2 RNA from the N gene at significant titers (57 to 303 copies per ml of sewage) in the period from 18 to 25 March 2020 using RT-qPCR. We validated detection of SARS-CoV-2 by Sanger sequencing the PCR product from the S gene. Viral titers observed were significantly higher than expected based on clinically confirmed cases in Massachusetts as of 25 March. Our approach is scalable and may be useful in modeling the SARS-CoV-2 pandemic and future outbreaks. IMPORTANCE Wastewater-based surveillance is a promising approach for proactive outbreak monitoring. SARS-CoV-2 is shed in stool early in the clinical course and infects a large asymptomatic population, making it an ideal target for wastewater-based monitoring. In this study, we develop a laboratory protocol to quantify viral titers in raw sewage via qPCR analysis and validate results with sequencing analysis. Our results suggest that the number of positive cases estimated from wastewater viral titers is orders of magnitude greater than the number of confirmed clinical cases and therefore may significantly impact efforts to understand the case fatality rate and progression of disease. These data may help inform decisions surrounding the advancement or scale-back of social distancing and quarantine efforts based on dynamic wastewater catchment-level estimations of prevalence.
- Published
- 2020
- Full Text
- View/download PDF
26. SARS-CoV-2 titers in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases
- Author
-
Newsha Ghaeli, Megan A. Brown, Mariana Matus, Claire Duvallet, Janelle R. Thompson, Stefan Wuertz, Jianbo Zhang, Federica Armas, Fuqing Wu, Richard Bonneau, Amy Xiao, Kyle A. McElroy, William P. Hanage, Mauricio Santillana, Steven F Rhode, Joshua A. Tucker, Katelyn Foppe, Jonathan Nagler, Xiaoqiong Gu, Katherine H. Huang, Eric J. Alm, Mary Bushman, Katya Moniz, Noriko Endo, Shijie Zhao, Wei Lin Lee, Peter R. Chai, and Timothy B. Erickson
- Subjects
Coronavirus disease 2019 (COVID-19) ,business.industry ,Applied and Environmental Science ,SARS-CoV-2 ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,COVID-19 prevalence ,Editor's Pick ,Article ,Titer ,Wastewater ,Clinical diagnosis ,Immunology ,PMMoV ,Medicine ,Symptom onset ,Viral shedding ,business ,viral titers ,Disease transmission ,wastewater ,Research Article - Abstract
Wastewater-based surveillance is a promising approach for proactive outbreak monitoring. SARS-CoV-2 is shed in stool early in the clinical course and infects a large asymptomatic population, making it an ideal target for wastewater-based monitoring. In this study, we develop a laboratory protocol to quantify viral titers in raw sewage via qPCR analysis and validate results with sequencing analysis. Our results suggest that the number of positive cases estimated from wastewater viral titers is orders of magnitude greater than the number of confirmed clinical cases and therefore may significantly impact efforts to understand the case fatality rate and progression of disease. These data may help inform decisions surrounding the advancement or scale-back of social distancing and quarantine efforts based on dynamic wastewater catchment-level estimations of prevalence., Wastewater surveillance represents a complementary approach to clinical surveillance to measure the presence and prevalence of emerging infectious diseases like the novel coronavirus SARS-CoV-2. This innovative data source can improve the precision of epidemiological modeling to understand the penetrance of SARS-CoV-2 in specific vulnerable communities. Here, we tested wastewater collected at a major urban treatment facility in Massachusetts and detected SARS-CoV-2 RNA from the N gene at significant titers (57 to 303 copies per ml of sewage) in the period from 18 to 25 March 2020 using RT-qPCR. We validated detection of SARS-CoV-2 by Sanger sequencing the PCR product from the S gene. Viral titers observed were significantly higher than expected based on clinically confirmed cases in Massachusetts as of 25 March. Our approach is scalable and may be useful in modeling the SARS-CoV-2 pandemic and future outbreaks. IMPORTANCE Wastewater-based surveillance is a promising approach for proactive outbreak monitoring. SARS-CoV-2 is shed in stool early in the clinical course and infects a large asymptomatic population, making it an ideal target for wastewater-based monitoring. In this study, we develop a laboratory protocol to quantify viral titers in raw sewage via qPCR analysis and validate results with sequencing analysis. Our results suggest that the number of positive cases estimated from wastewater viral titers is orders of magnitude greater than the number of confirmed clinical cases and therefore may significantly impact efforts to understand the case fatality rate and progression of disease. These data may help inform decisions surrounding the advancement or scale-back of social distancing and quarantine efforts based on dynamic wastewater catchment-level estimations of prevalence.
- Published
- 2020
27. SARS-CoV-2 titers in wastewater are higher than expected from clinically confirmed cases
- Author
-
Amy Xiao, Newsha Ghaeli, Peter R. Chai, Kathryn M. Kauffman, Wei Lin Lee, Claire Duvallet, Eric J. Alm, Katya Moniz, Mariana Matus, Jianbo Zhang, Xiaoqiong Gu, Timothy B. Erickson, William P. Hanage, Janelle R. Thompson, Fuqing Wu, and Noriko Endo
- Subjects
Titer ,Wastewater ,business.industry ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Pandemic ,Pcr cloning ,Outbreak ,Medicine ,business ,Virology - Abstract
Wastewater surveillance may represent a complementary approach to measure the presence and even prevalence of infectious diseases when the capacity for clinical testing is limited. Moreover, aggregate, population-wide data can help inform modeling efforts. We tested wastewater collected at a major urban treatment facility in Massachusetts and found the presence of SARS-CoV-2 at high titers in the period from March 18 - 25 using RT-qPCR. We then confirmed the identity of the PCR product by direct DNA sequencing. Viral titers observed were significantly higher than expected based on clinically confirmed cases in Massachusetts as of March 25. The reason for the discrepancy is not yet clear, and until further experiments are complete, these data do not necessarily indicate that clinical estimates are incorrect. Our approach is scalable and may be useful in modeling the SARS-CoV-2 pandemic and future outbreaks.
- Published
- 2020
28. SARS-CoV-2 RNA concentrations in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases
- Author
-
Mariana Matus, Peter R. Chai, Newsha Ghaeli, Timothy B. Erickson, Richard Bonneau, Amy Xiao, Xiaoqiong Gu, Mauricio Santillana, Katya Moniz, Steven F Rhode, Katelyn Foppe, Shijie Zhao, William P. Hanage, Kyle A. McElroy, Janelle R. Thompson, Fuqing Wu, Wei Lin Lee, Joshua A. Tucker, Mary Bushman, Katherine H. Huang, Noriko Endo, Federica Armas, Jonathan Nagler, Eric J. Alm, Jianbo Zhang, Megan A. Brown, Claire Duvallet, and Stefan Wuertz
- Subjects
Environmental Engineering ,Coronavirus disease 2019 (COVID-19) ,viruses ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Wastewater ,Article ,Humans ,Environmental Chemistry ,Medicine ,Symptom onset ,Viral shedding ,Waste Management and Disposal ,SARS-CoV-2 ,business.industry ,COVID-19 ,Pollution ,Virus Shedding ,Clinical diagnosis ,Immunology ,Longitudinal ,RNA, Viral ,Foreshadow ,business ,Convolution model ,Viral load ,Disease transmission ,Wastewater surveillance - Abstract
Current estimates of COVID-19 prevalence are largely based on symptomatic, clinically diagnosed cases. The existence of a large number of undiagnosed infections hampers population-wide investigation of viral circulation. Here, we quantify the SARS-CoV-2 concentration and track its dynamics in wastewater at a major urban wastewater treatment facility in Massachusetts, between early January and May 2020. SARS-CoV-2 was first detected in wastewater on March 3. SARS-CoV-2 RNA concentrations in wastewater correlated with clinically diagnosed new COVID-19 cases, with the trends appearing 4–10 days earlier in wastewater than in clinical data. We inferred viral shedding dynamics by modeling wastewater viral load as a convolution of back-dated new clinical cases with the average population-level viral shedding function. The inferred viral shedding function showed an early peak, likely before symptom onset and clinical diagnosis, consistent with emerging clinical and experimental evidence. This finding suggests that SARS-CoV-2 concentrations in wastewater may be primarily driven by viral shedding early in infection. This work shows that longitudinal wastewater analysis can be used to identify trends in disease transmission in advance of clinical case reporting, and infer early viral shedding dynamics for newly infected individuals, which are difficult to capture in clinical investigations., Graphical abstract Unlabelled Image
- Published
- 2022
29. Geospatial distribution of viromes in tropical freshwater ecosystems
- Author
-
Karina Yew-Hoong Gin, Nazanin Saeidi, Qi Xiang Martin Tay, Shu Harn Te, Janelle R. Thompson, Xiaoqiong Gu, Ariel Kushmaro, and Shin Giek Goh
- Subjects
0301 basic medicine ,Geospatial distribution ,Environmental Engineering ,food.ingredient ,Fresh Water ,Freshwater ecosystem ,Article ,03 medical and health sciences ,food ,Caudovirales ,Abundance (ecology) ,Mimiviridae ,Human virome ,Waste Management and Disposal ,Relative species abundance ,Water Science and Technology ,Civil and Structural Engineering ,Dicistroviridae ,Singapore ,Spatial Analysis ,Diversity ,biology ,Virome ,Ecology ,Ecological Modeling ,Freshwater ecosystems ,Human-related viruses ,biology.organism_classification ,Pollution ,030104 developmental biology ,Cyclovirus ,Viruses ,Land use ,Environmental Monitoring - Abstract
This study seeks to understand the general distribution of virome abundance and diversity in tropical freshwater ecosystems in Singapore and the geospatial distribution of the virome under different landuse patterns. Correlations between diversity, environmental parameters and land use patterns were analyzed and significant correlations were highlighted. Overall, the majority (65.5%) of the annotated virome belonged to bacteriophages. The percentage of Caudovirales was higher in reservoirs whereas the percentages of Dicistroviridae, Microviridae and Circoviridae were higher in tributaries. Reservoirs showed a higher Shannon-index virome diversity compared to upstream tributaries. Land use (urbanized, agriculture and parkland areas) influenced the characteristics of the virome distribution pattern. Dicistroviridae and Microviridae were enriched in urbanized tributaries while Mimiviridae, Phycodnaviridae, Siphoviridae and Podoviridae were enriched in parkland reservoirs. Several sequences closely related to the emerging zoonotic virus, cyclovirus, and the human-related virus (human picobirnavirus), were also detected. In addition, the relative abundance of PMMoV (pepper mild mottle virus) sequences was significantly correlated with RT-qPCR measurements (0.588, Graphical abstract Image 1, Highlights • Land use is the main driver of the viral community structure in surface waters. • 66 viral families were detected and 66% of the annotated virome was bacteriophages. • Reservoirs showed a higher Shannon diversity (10.4) than upstream tributaries (8.4). • Sequences closely related to human picobirnavirus and cyclovirus were detected. • The relative abundance of PMMoV sequences was correlated with RT-qPCR measurements.
- Published
- 2018
30. Wastewater surveillance of SARS-CoV-2 across 40 U.S. states from February to June 2020
- Author
-
Mariana Matus, Timothy B. Erickson, Janelle R. Thompson, Eric J. Alm, Katya Moniz, Jianbo Zhang, Newsha Ghaeli, Peter R. Chai, Mary Bushman, William P. Hanage, Fuqing Wu, Noriko Endo, Amy Xiao, Wei Lin Lee, Steven F Rhode, Federica Armas, Katherine H. Huang, Xiaoqiong Gu, Katelyn Foppe, Claire Duvallet, Stefan Wuertz, and Kyle A. McElroy
- Subjects
Disease surveillance ,education.field_of_study ,Environmental Engineering ,Coronavirus disease 2019 (COVID-19) ,SARS-CoV-2 ,Ecological Modeling ,Incidence (epidemiology) ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Population ,Detection rate ,Outbreak ,Pollution ,Article ,United States ,Geography ,Wastewater ,Environmental health ,Spatiotemporal dynamics ,Sewage treatment ,education ,Waste Management and Disposal ,Wastewater surveillance ,Water Science and Technology ,Civil and Structural Engineering - Abstract
Wastewater-based disease surveillance is a promising approach for monitoring community outbreaks. Here we describe a nationwide campaign to monitor SARS-CoV-2 in the wastewater of 159 counties in 40 U.S. states, covering 13% of the U.S. population from February 18 to June 2, 2020. Out of 1,751 total samples analyzed, 846 samples were positive for SARS-CoV-2 RNA, with overall viral concentrations declining from April to May. Wastewater viral titers were consistent with, and appeared to precede, clinical COVID-19 surveillance indicators, including daily new cases. Wastewater surveillance had a high detection rate (>80%) of SARS-CoV-2 when the daily incidence exceeded 13 per 100,000 people. Detection rates were positively associated with wastewater treatment plant catchment size. To our knowledge, this work represents the largest-scale wastewater-based SARS-CoV-2 monitoring campaign to date, encompassing a wide diversity of wastewater treatment facilities and geographic locations. Our findings demonstrate that a national wastewater-based approach to disease surveillance may be feasible and effective., Graphical Abstract Image, graphical abstract
- Published
- 2021
31. Variation of Bacterial Communities with Water Quality in an Urban Tropical Catchment
- Author
-
Jean Pierre Nshimyimana, Adam J. E. Freedman, Janelle R. Thompson, Lloyd Hc Chua, and Peter Shanahan
- Subjects
0301 basic medicine ,Microorganism ,030106 microbiology ,Drainage basin ,Indicator bacteria ,Feces ,03 medical and health sciences ,Abundance (ecology) ,RNA, Ribosomal, 16S ,Water Quality ,Escherichia coli ,Environmental Chemistry ,Cities ,Tropical Climate ,geography ,geography.geographical_feature_category ,Sewage ,biology ,Bacteroidetes ,Ecology ,Community structure ,Tropics ,General Chemistry ,biology.organism_classification ,Bacteroidales ,Water quality - Abstract
A major challenge for assessment of water quality in tropical environments is the natural occurrence and potential growth of Fecal Indicator Bacteria (FIB). To gain a better understanding of the relationship between measured levels of FIB and the distribution of sewage-associated bacteria, including potential pathogens, in the tropics this study compared the abundance of FIB (Total coliforms and E. coli) and the Bacteroidales (HF183 marker) with bacterial community structure determined by next-generation amplicon sequencing. Water was sampled twice over 6 months from 18 sites within a tropical urban catchment and reservoir, followed by extraction of DNA from microorganisms, and sequencing targeting the V3-V4 region of the 16S rRNA gene. Multivariate statistical analyses indicated that bacterial community composition (BCC) varied between reservoir and catchment, within catchment land-uses, and with E. coli concentration. Beta-regression indicated that the proportion of sequences from sewage-associated taxa (SAT) or pathogen-like sequences (PLS) were predicted most significantly by measured levels of E. coli(log MPN/100 mL) (χ
- Published
- 2017
32. Field Observations, Experimental Studies, and Thermodynamic Modeling of CO2 Effects on Microbial Populations
- Author
-
Adam J. E. Freedman, Janelle R. Thompson, Kyle C. Peet, and Jonathan B. Ajo-Franklin
- Subjects
Biogeochemical cycle ,Microbial population biology ,Microorganism ,Environmental chemistry ,Environmental science ,Mineralization (soil science) ,Carbon sequestration ,Carbon cycle ,Ground water quality - Abstract
Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface, generating biomass and extracellular materials. Following geologic carbon dioxide sequestration (GCS), subsurface microorganisms may influence the fate of injected supercritical (sc) CO 2 , as well as mediate secondary reactions relevant to mineralization and ground water quality. This chapter will review the current state of knowledge concerning the microbiology of GCS including the potential effects of injected scCO 2 on subsurface microbial cells, populations, and communities, and microbiological feedbacks relevant to the evolution of brine chemistry, mineral surfaces, and changes in porosity. Recent work including thermodynamic modeling, field observations of CO 2 injection, observations from natural analog sites, and laboratory model systems, shed light on the microbial populations and biogeochemical transformations expected after GCS. Modern molecular and genomics tools have revealed potential physiological and metabolic strategies for microbial community function under conditions associated with GCS. These studies advance our understanding of microbial processes during GCS and enable further development of bio-based interventions that may help to de-risk and optimize implementation of GCS at large scale.
- Published
- 2019
33. Making waves: Wastewater surveillance of SARS-CoV-2 for population-based health management
- Author
-
Lee Ching Ng, Monamie Bhadra Haines, Yarlagadda V. Nancharaiah, Janelle R. Thompson, Wei Lin Lee, Stefan Wuertz, Xiaoqiong Gu, Verónica Beatriz Rajal, Rosina Girones, Eric J. Alm, Asian School of the Environment, School of Civil and Environmental Engineering, Singapore Centre for Environmental Life Sciences and Engineering, and CREATE
- Subjects
medicine.medical_specialty ,Environmental Engineering ,DATA PRIVACY ,Pneumonia, Viral ,0208 environmental biotechnology ,Population ,Otras Ingeniería del Medio Ambiente ,INGENIERÍAS Y TECNOLOGÍAS ,Wastewater Surveillance ,02 engineering and technology ,Disease ,Wastewater ,010501 environmental sciences ,FECAL-ORAL TRANSMISSION ,01 natural sciences ,Article ,Fecal-oral transmission ,Betacoronavirus ,Environmental health ,Sewerage ,medicine ,Humans ,Ingeniería del Medio Ambiente ,education ,Pandemics ,Waste Management and Disposal ,health care economics and organizations ,0105 earth and related environmental sciences ,Water Science and Technology ,Civil and Structural Engineering ,HEALTH MANAGEMENT ,education.field_of_study ,Disease surveillance ,Health management system ,SARS-CoV-2 ,Ecological Modeling ,Public health ,COVID-19 ,Pollution ,Environmental engineering [Engineering] ,020801 environmental engineering ,Ecological Modelling ,Health management ,Sample collection ,Business ,Coronavirus Infections ,Data privacy ,Wastewater surveillance - Abstract
Highlights • Wastewater surveillance cheaper and less invasive than massive testing of individuals. • Useful early alert of viral circulation to prevent outbreaks and inform policy decisions. • Success of surveillance requires public legitimacy and trust of such measures., Worldwide, clinical data remain the gold standard for disease surveillance and tracking. However, such data are limited due to factors such as reporting bias and inability to track asymptomatic disease carriers. Disease agents are excreted in the urine and feces of infected individuals regardless of disease symptom severity. Wastewater surveillance – that is, monitoring disease via human effluent – represents a valuable complement to clinical approaches. Because wastewater is relatively inexpensive and easy to collect and can be monitored at different levels of population aggregation as needed, wastewater surveillance can offer a real-time, cost-effective view of a community's health that is independent of biases associated with case-reporting. For SARS-CoV-2 and other disease-causing agents we envision an aggregate wastewater-monitoring system at the level of a wastewater treatment plant and exploratory or confirmatory monitoring of the sewerage system at the neighborhood scale to identify or confirm clusters of infection or assess impact of control measures where transmission has been established. Implementation will require constructing a framework with collaborating government agencies, public or private utilities, and civil society organizations for appropriate use of data collected from wastewater, identification of an appropriate scale of sample collection and aggregation to balance privacy concerns and risk of stigmatization with public health preservation, and consideration of the social implications of wastewater surveillance.
- Published
- 2020
34. Variably improved microbial source tracking with digital droplet PCR
- Author
-
Jean Pierre Nshimyimana, Mercedes Cecilia Cruz, Janelle R. Thompson, Stefan Wuertz, School of Civil and Environmental Engineering, and Singapore Centre for Environmental Life Sciences and Engineering (SCELSE)
- Subjects
Environmental Engineering ,Animal feces ,0208 environmental biotechnology ,Sewage ,02 engineering and technology ,010501 environmental sciences ,QUANTITATIVE PCR ,Real-Time Polymerase Chain Reaction ,01 natural sciences ,Sensitivity and Specificity ,Feces ,Environmental water ,Animals ,Humans ,Food science ,Waste Management and Disposal ,Digital droplet pcr ,0105 earth and related environmental sciences ,Water Science and Technology ,Civil and Structural Engineering ,Microbial source tracking ,Digital Droplet PCR ,biology ,purl.org/becyt/ford/2.8 [https] ,business.industry ,Bacteroidetes ,Ecological Modeling ,Reproducibility of Results ,biology.organism_classification ,Pollution ,Bacteroidales ,020801 environmental engineering ,Environmental engineering [Engineering] ,GENETIC MARKERS ,purl.org/becyt/ford/2 [https] ,Genetic marker ,business ,Microbial Source Tracking - Abstract
This study addressed whether digital droplet PCR (ddPCR) could improve sensitivity and specificity of human-associated Bacteroidales genetic markers, BacHum and B. theta, and their quantification in environmental and fecal composite samples. Human markers were quantified by qPCR and ddPCR platforms obtained from the same manufacturer. A total of 180 samples were evaluated by each platform including human and animal feces, sewage, and environmental water. The sensitivity of ddPCR and qPCR marker assays in sewage and human stool was 0.85–1.00 with marginal reduction in human stool by ddPCR relative to qPCR (
- Published
- 2017
35. Microbial Growth under Supercritical CO 2
- Author
-
Janelle R. Thompson, Hector H. Hernandez, Vanya Britto, Kyle C. Peet, Chris Boreham, Jonathan B. Ajo-Franklin, and Adam J. E. Freedman
- Subjects
DNA, Bacterial ,Bacillus safensis ,Carbon Sequestration ,Geologic Sediments ,Bacillus amyloliquefaciens ,Microorganism ,Molecular Sequence Data ,Microbial metabolism ,Bacillus cereus ,Bacillus ,Bacterial growth ,Polymerase Chain Reaction ,Applied Microbiology and Biotechnology ,Microbiology ,Bioreactors ,RNA, Ribosomal, 16S ,Environmental Microbiology ,Bacillus megaterium ,Ecology ,biology ,fungi ,Sequence Analysis, DNA ,Carbon Dioxide ,biology.organism_classification ,bacteria ,Bacteria ,Food Science ,Biotechnology - Abstract
Growth of microorganisms in environments containing CO 2 above its critical point is unexpected due to a combination of deleterious effects, including cytoplasmic acidification and membrane destabilization. Thus, supercritical CO 2 (scCO 2 ) is generally regarded as a sterilizing agent. We report isolation of bacteria from three sites targeted for geologic carbon dioxide sequestration (GCS) that are capable of growth in pressurized bioreactors containing scCO 2 . Analysis of 16S rRNA genes from scCO 2 enrichment cultures revealed microbial assemblages of varied complexity, including representatives of the genus Bacillus . Propagation of enrichment cultures under scCO 2 headspace led to isolation of six strains corresponding to Bacillus cereus , Bacillus subterraneus , Bacillus amyloliquefaciens , Bacillus safensis , and Bacillus megaterium . Isolates are spore-forming, facultative anaerobes and capable of germination and growth under an scCO 2 headspace. In addition to these isolates, several Bacillus type strains grew under scCO 2 , suggesting that this may be a shared feature of spore-forming Bacillus spp. Our results provide direct evidence of microbial activity at the interface between scCO 2 and an aqueous phase. Since microbial activity can influence the key mechanisms for permanent storage of sequestered CO 2 (i.e., structural, residual, solubility, and mineral trapping), our work suggests that during GCS microorganisms may grow and catalyze biological reactions that influence the fate and transport of CO 2 in the deep subsurface.
- Published
- 2015
36. Genomics insights into production of 2-methylisoborneol and a putative cyanobactin by Planktothricoides sp. SR001
- Author
-
Janelle R. Thompson, Karina Yew-Hoong Gin, Shu Harn Te, BoonFei Tan, and Chek Yin Boo
- Subjects
0301 basic medicine ,Whole genome sequencing ,Genetics ,2-methylisoborneol ,lcsh:QH426-470 ,Planktothricoides ,Operon ,Strain (biology) ,Metabolite ,Genomics ,Biology ,Genome ,lcsh:Genetics ,03 medical and health sciences ,chemistry.chemical_compound ,Viridisamide A ,030104 developmental biology ,Cyanobactin ,chemistry ,Biosynthesis ,Phormidiaceae ,Extended Genome Report ,Gene - Abstract
Planktothricoides is a free-living filamentous cyanobacterium belonging to the order Oscillatoriales and the family Phormidiaceae, capable of forming bloom in fresh and brackish waters. A unicyanobacterial non-axenic culture dominated by Planktothricoides sp. SR001 was obtained from a freshwater reservoir in Singapore. The draft genome presented here is the first tropical freshwater Planktothricoides sp. ever sequenced. The genome of 7.0Mbp contains 5,776 genes predicted using the JGI IMG pipeline. The whole genome sequence allows identification of genes encoding for nitrogen-fixation, accessory photosynthetic pigments and biosynthesis of an off-flavor compound, 2-methylisoborneol, which has been experimentally verified here based on metabolite detection. In addition, strain SR001 genome contains an operon putatively involved in the production of a linear tripeptide cyanobactin related to viridisamide A and aeruginosamide, with the later known to possess anti-microbial or cytotoxic effect.
- Published
- 2017
37. Relationship of Microbiota and Cyanobacterial Secondary Metabolites in Planktothricoides-Dominated Bloom
- Author
-
Karina Yew-Hoong Gin, Janelle R. Thompson, BoonFei Tan, and Shu Harn Te
- Subjects
0301 basic medicine ,biology ,Ecology ,Microbiota ,fungi ,030106 microbiology ,Community structure ,Fresh Water ,General Chemistry ,Eutrophication ,Synechococcus ,biology.organism_classification ,Cyanobacteria ,03 medical and health sciences ,RNA, Ribosomal, 16S ,Phytoplankton ,Environmental Chemistry ,Water quality ,Proteobacteria ,Bloom ,Diel vertical migration - Abstract
The identification of phytoplankton species and microbial biodiversity is necessary to assess water ecosystem health and the quality of water resources. We investigated the short-term (2 days) vertical and diel variations in bacterial community structure and microbially derived secondary metabolites during a cyanobacterial bloom that emerged in a highly urbanized tropical reservoir. The waterbody was largely dominated by the cyanobacteria Planktothricoides spp., together with the Synechococcus, Pseudanabaena, Prochlorothrix, and Limnothrix. Spatial differences (i.e., water depth) rather than temporal differences (i.e., day versus night) better-explained the short-term variability in water quality parameters and bacterial community composition. Difference in bacterial structure suggested a resource-driven distribution pattern for the community. We found that the freshwater bacterial community associated with cyanobacterial blooms is largely conserved at the phylum level, with Proteobacteria (β-proteobateria), Bacteroidetes, and Actinobacteria as the main taxa despite the cyanobacterial species present and geographical (Asia, Europe, Australia, and North America) or climatic distinctions. Through multivariate statistical analyses of the bacterial community, environmental parameters, and secondary metabolite concentrations, we observed positive relationships between the occurrences of cyanobacterial groups and off-flavor compounds (2-methyisoborneol and β-ionone), suggesting a cyanobacterial origin. This study demonstrates the potential of 16S rRNA gene amplicon sequencing as a supporting tool in algal bloom monitoring or water-resource management.
- Published
- 2017
38. Distribution and abundance of human-specific Bacteroides and relation to traditional indicators in an urban tropical catchment
- Author
-
Janelle R. Thompson, Jean Pierre Nshimyimana, Peter Shanahan, Eveline Ekklesia, Lloyd H.C. Chua, and School of Civil and Environmental Engineering
- Subjects
Genetic Markers ,Watershed ,environmental contamination ,Sewage ,Biology ,Applied Microbiology and Biotechnology ,water quality ,Polymerase Chain Reaction ,Engineering::Environmental engineering [DRNTU] ,Feces ,RNA, Ribosomal, 16S ,Tropical climate ,Escherichia coli ,Bacteroides ,Phylogeny ,Singapore ,Tropical Climate ,Land use ,business.industry ,Ecology ,source tracking ,General Medicine ,Original Articles ,Phylogenetic diversity ,Genetic marker ,Sewage treatment ,Water quality ,business ,Water Microbiology ,Biotechnology - Abstract
Aims: The study goals were to determine the relationship between faecal indicator bacteria (FIB), the HF183 marker and land use, and the phylogenetic diversity of HF183 marker sequences in a tropical urban watershed. Methods and Results: Total coliforms, Escherichia coli, and HF183 were quantified in 81 samples categorized as undeveloped, residential and horticultural from the Kranji Reservoir and Catchment in Singapore. Quantitative-PCR for HF183 followed by analysis of variance indicated that horticultural areas had significantly higher geometric means for marker levels (4·3 × 104 HF183-GE 100 ml−1) than nonhorticultural areas (3·07 × 103 HF183-GE 100 ml−1). E. coli and HF183 were moderately correlated in horticultural areas (R = 0·59, P = 0·0077), but not elsewhere in the catchment. Initial upstream surveys of candidate sources revealed elevated HF183 in a wastewater treatment effluent but not in aquaculture ponds. The HF183 marker was cloned, sequenced and determined by phylogenetic analysis to match the original marker description. Conclusion: We show that quantification of the HF183 marker is a useful tool for mapping the spatial distribution and potential sources of human sewage contamination in tropical environments such as Singapore. Significance and Impact: A major challenge for assessment of water quality in tropical environments is the natural occurrence and nonconservative behaviour of FIB. The HF183 marker has been employed in temperate environments as an alternative indicator for human sewage contamination. Our study supports the use of the HF183 marker as an indicator for human sewage in Singapore and motivates further work to determine HF183 marker levels that correspond to public health risk in tropical environments. NRF (Natl Research Foundation, S’pore) Published version
- Published
- 2014
39. Draft Genome Sequence of Cylindrospermopsis sp. Strain CR12 Extracted from the Minimetagenome of a Nonaxenic Unialgal Culture from a Tropical Freshwater Lake
- Author
-
Janelle R. Thompson, Karina Yew-Hoong Gin, BoonFei Tan, Nur Hazimah Mohamed Nor, and Shu Harn Te
- Subjects
0106 biological sciences ,0301 basic medicine ,Whole genome sequencing ,biology ,010604 marine biology & hydrobiology ,Strain (biology) ,Cylindrospermopsis ,biology.organism_classification ,01 natural sciences ,03 medical and health sciences ,chemistry.chemical_compound ,030104 developmental biology ,chemistry ,Botany ,Genetics ,Cylindrospermopsin ,Prokaryotes ,Molecular Biology - Abstract
Cylindrospermopsis is known to be one of the major bloom-forming cyanobacterial genera in many freshwater environments. We report here the draft genome sequence of a tropical Cylindrospermopsis sp. strain, CR12, which is capable of producing the hepatotoxic cylindrospermopsin.
- Published
- 2016
40. Insights from the draft genome of the subsection V (Stigonematales) cyanobacterium Hapalosiphon sp. Strain MRB220 associated with 2-MIB production
- Author
-
BoonFei Tan, Chek Yin Boo, Karina Yew-Hoong Gin, Janelle R. Thompson, Shu Harn Te, Massachusetts Institute of Technology. Department of Civil and Environmental Engineering, Singapore-MIT Alliance in Research and Technology (SMART), Tan, Boon Fei, and Thompson, Janelle Renee
- Subjects
0301 basic medicine ,Cyanobacteria ,Geosmin synthase ,030106 microbiology ,Secondary metabolite ,Genome ,Hapalosiphon ,03 medical and health sciences ,Stigonematales ,Botany ,Genetics ,medicine ,Extended Genome Report ,Gene ,Whole genome sequencing ,biology ,Strain (biology) ,2-MIB ,16S ribosomal RNA ,biology.organism_classification ,030104 developmental biology ,Subsection V cyanobacterium ,Fischerella ,medicine.drug ,Filamentous heterocysts - Abstract
A non-axenic unialgal culture containing a Subsection V (Stigonematales) cyanobacterium, Hapalosiphon strain MRB 220, was obtained from a benthic freshwater algal mat through multiple transfers following growth in sterile media. Physiological characterization demonstrated the culture was capable of nitrogen-fixation and production of the off flavor compound 2-methylisoborneol (2-MIB). Total DNA isolated from this culture was sequenced using Illumina HiSeq and de novo assembled into contigs. The genome of MRB 220 was separated from co-occurring heterotrophic bacteria using sequence homology and compositional approaches, and its purity was confirmed based on best BLAST hit classification and principle component analysis of the tetranucleotide frequencies of fragmented contigs. The genome of ~7.4 Mbp contains 6,345 protein coding genes with 4,320 of these having functional prediction including predicted pathways for biosynthesis of the secondary metabolite welwitindolinone. Analyses of 16S rRNA gene and whole genome sequence average nucleotide identity indicated close relatedness of MRB 220 to the genera Hapalosiphon and Fischerella within the order Stigonematales. Microscopic examination showed that MRB 220 formed heterocystous branched filaments, thereby supporting identification of strain MRB 220 as a morphospecies of Hapalosiphon. Availability of the draft genome of Hapalosiphon strain MRB 220 enables future work to elucidate the pathway and dynamics for biosynthesis of 2-MIB and other secondary metabolites and understand the ecology and physiology of Stigonematales cyanobacteria in tropical freshwaters., Singapore. National Research Foundation (under its Environmental & Water Technologies Strategic Research Programme and administered by the Environment & Water Industry Programme Office (EWI) of the PUB (Grant number: 1102-IRIS-14-02)), Singapore. National Research Foundation (Singapore MIT Alliance for Research and Technology’s (SMART) Center for Environmental Sensing and Modeling (CENSAM) research program)
- Published
- 2015
41. Cover Feature: Extraction Rate and Energy Efficiency of Supercritical Carbon Dioxide Recovery of Higher Alcohols from Dilute Aqueous Solution (Energy Technol. 4/2018)
- Author
-
Geoffrey A. Tompsett, Jason T. Boock, Cameron DiSpirito, Eric Stolz, David R. Knutson, Allison G. Rivard, Mark R. Overdevest, Chelsea N. Conlon, Kristala L. J. Prather, Janelle R. Thompson, and Michael T. Timko
- Subjects
General Energy - Published
- 2018
42. Microbial diversity and activity in the Nematostella vectensis holobiont: insights from 16S rRNA gene sequencing, isolate genomes, and a pilot-scale survey of gene expression
- Author
-
Kevin Penn, Ju Hyoung Lim, Samodha C. Fernando, Adam M. Reitzel, Jia Yi Har, Janelle R. Thompson, Tim Helbig, Massachusetts Institute of Technology. Department of Civil and Environmental Engineering, Har, Jia Y., Helbig, Tim, Lim, Ju H., Fernando, Samodha C., Penn, Kevin, and Thompson, Janelle Renee
- Subjects
Microbiology (medical) ,Campylobacterales ,food.ingredient ,lcsh:QR1-502 ,Nematostella vectensis ,Stappia ,Nematostella ,Pseudomonas oleovorans ,Cnidarian ,phasins ,Microbiology ,Genome ,lcsh:Microbiology ,food ,mixotrophy ,cnidaria ,microbiota ,Original Research ,holobiont ,Genetics ,biology ,Ecology ,Starlet sea anemone ,16S ribosomal RNA ,biology.organism_classification ,Holobiont - Abstract
We have characterized the molecular and genomic diversity of the microbiota of the starlet sea anemone Nematostella vectensis, a cnidarian model for comparative developmental and functional biology and a year-round inhabitant of temperate salt marshes. Molecular phylogenetic analysis of 16S rRNA gene clone libraries revealed four ribotypes associated with N. vectensis at multiple locations and times. These associates include two novel ribotypes within the ε-Proteobacterial order Campylobacterales and the Spirochetes, respectively, each sharing 99% 16S rRNA identity with Endozoicomonas elysicola and Pseudomonas oleovorans, respectively. Species-specific PCR revealed that these populations persisted in N. vectensis asexually propagated under laboratory conditions. cDNA indicated expression of the Campylobacterales and Endozoicomonas 16S rRNA in anemones from Sippewissett Marsh, MA. A collection of bacteria from laboratory raised N. vectensis was dominated by isolates from P. oleovorans and Rhizobium radiobacter. Isolates from field-collected anemones revealed an association with Limnobacter and Stappia isolates. Genomic DNA sequencing was carried out on 10 cultured bacterial isolates representing field- and laboratory-associates, i.e., Limnobacter spp., Stappia spp., P. oleovorans and R. radiobacter. Genomes contained multiple genes identified as virulence (host-association) factors while S. stellulata and L. thiooxidans genomes revealed pathways for mixotrophic sulfur oxidation. A pilot metatranscriptome of laboratory-raised N. vectensis was compared to the isolate genomes and indicated expression of ORFs from L. thiooxidans with predicted functions of motility, nutrient scavenging (Fe and P), polyhydroxyalkanoate synthesis for carbon storage, and selective permeability (porins). We hypothesize that such activities may mediate acclimation and persistence of bacteria in a N. vectensis holobiont defined by both internal and external gradients of chemicals and nutrients in a dynamic coastal habitat., Massachusetts Institute of Technology. Department of Civil and Environmental Engineering, National Science Foundation (U.S.). Graduate Research Fellowship, National Research Foundation of Korea (Fellowship)
- Published
- 2015
43. Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities
- Author
-
Lay Leng Loh, Jean Pierre Nshimyimana, Charmaine Ng, BoonFei Tan, Karina Yew-Hoong Gin, Janelle R. Thompson, Massachusetts Institute of Technology. Department of Civil and Environmental Engineering, Thompson, Janelle Renee, School of Civil and Environmental Engineering, and Singapore Centre for Environmental Life Sciences Engineering
- Subjects
Microbiology (medical) ,antibiotic resistance ,Ecology (disciplines) ,Harmful Algal Bloom ,Waterquality ,lcsh:QR1-502 ,Sewage ,Next-generationsequencing ,Review ,Biology ,Microbiology ,DNA sequencing ,lcsh:Microbiology ,Water Quality ,Chemical contaminants ,Pollutant ,fecal indicator ,business.industry ,Fecalindicator ,Biotechnology ,Metagenomics ,Harmfulalgalbloom ,Biodegradation ,Next-generation sequencing ,Biochemical engineering ,Water quality ,business ,Bioindicator ,Antibioticresistance - Abstract
Water quality is an emergent property of a complex system comprised of interacting microbial populations and introduced microbial and chemical contaminants. Studies leveraging next-generation sequencing (NGS) technologies are providing new insights into the ecology of microbially mediated processes that influence fresh water quality such as algal blooms, contaminant biodegradation, and pathogen dissemination. In addition, sequencing methods targeting small subunit (SSU) rRNA hypervariable regions have allowed identification of signature microbial species that serve as bioindicators for sewage contamination in these environments. Beyond amplicon sequencing, metagenomic and metatranscriptomic analyses of microbial communities in fresh water environments reveal the genetic capabilities and interplay of waterborne microorganisms, shedding light on the mechanisms for production and biodegradation of toxins and other contaminants. This review discusses the challenges and benefits of applying NGS-based methods to water quality research and assessment. We will consider the suitability and biases inherent in the application of NGS as a screening tool for assessment of biological risks and discuss the potential and limitations for direct quantitative interpretation of NGS data. Secondly, we will examine case studies from recent literature where NGS based methods have been applied to topics in water quality assessment, including development of bioindicators for sewage pollution and microbial source tracking, characterizing the distribution of toxin and antibiotic resistance genes in water samples, and investigating mechanisms of biodegradation of harmful pollutants that threaten water quality. Finally, we provide a short review of emerging NGS platforms and their potential applications to the next generation of water quality assessment tools., Singapore-MIT Alliance for Research and Technology. Center for Environmental Sensing and Modeling
- Published
- 2015
44. Draft Genome Sequences of Supercritical CO 2 -Tolerant Bacteria Bacillus subterraneus MITOT1 and Bacillus cereus MIT0214
- Author
-
Janelle R. Thompson, Kyle C. Peet, Massachusetts Institute of Technology. Department of Civil and Environmental Engineering, Peet, Kyle Creighton, and Thompson, Janelle Renee
- Subjects
0303 health sciences ,Bacilli ,Geologic sequestration ,Phylogenetic tree ,030306 microbiology ,fungi ,Bacillus cereus ,Biology ,biology.organism_classification ,Genome ,Supercritical fluid ,Bacillus subterraneus ,Microbiology ,03 medical and health sciences ,Genetics ,bacteria ,Prokaryotes ,Molecular Biology ,Bacteria ,030304 developmental biology - Abstract
We report draft genome sequences of Bacillus subterraneus MITOT1 and Bacillus cereus MIT0214 isolated through enrichment of samples from geologic sequestration sites in pressurized bioreactors containing a supercritical (sc) CO[subscript 2] headspace. Their genome sequences expand the phylogenetic range of sequenced bacilli and allow characterization of molecular mechanisms of scCO[subscript 2] tolerance., United States. Dept. of Energy. Office of Fossil Energy (Award DE-FE0002128), MIT Energy Initiative
- Published
- 2015
45. Extensive Variation in Intracellular Symbiont Community Composition among Members of a Single Population of the Wood-Boring Bivalve Lyrodus pedicellatus (Bivalvia: Teredinidae)
- Author
-
Wendy Morrill, Martin F. Polz, Yvette A. Luyten, Janelle R. Thompson, and Daniel L. Distel
- Subjects
DNA, Bacterial ,Gills ,animal structures ,Molecular Sequence Data ,Population ,Zoology ,DNA, Ribosomal ,Polymerase Chain Reaction ,Ribotyping ,Applied Microbiology and Biotechnology ,Microbial Ecology ,Phylogenetics ,RNA, Ribosomal, 16S ,Genetic variation ,Animals ,Cloning, Molecular ,Symbiosis ,education ,Clade ,Ecosystem ,Phylogeny ,DNA Primers ,Gene Library ,Phylotype ,education.field_of_study ,Bacteria ,Ecology ,biology ,Phylogenetic tree ,Host (biology) ,fungi ,Electrophoresis, Capillary ,Genetic Variation ,Sequence Analysis, DNA ,biology.organism_classification ,Bivalvia ,Proteobacteria ,Food Science ,Biotechnology - Abstract
Shipworms (wood-boring bivalves of the family Teredinidae ) harbor in their gills intracellular bacterial symbionts thought to produce enzymes that enable the host to consume cellulose as its primary carbon source. Recently, it was demonstrated that multiple genetically distinct symbiont populations coexist within one shipworm species, Lyrodus pedicellatus . Here we explore the extent to which symbiont communities vary among individuals of this species by quantitatively examining the diversity, abundance, and pattern of occurrence of symbiont ribotypes (unique 16S rRNA sequence types) among specimens drawn from a single laboratory-reared population. A total of 18 ribotypes were identified in two clone libraries generated from gill tissue of (i) a single specimen and (ii) four pooled specimens. Phylogenetic analysis assigned all of the ribotypes to a unique clade within the γ subgroup of proteobacteria which contained at least five well-supported internal clades (phylotypes). By competitive quantitative PCR and constant denaturant capillary electrophoresis, we estimated the number and abundance of symbiont phylotypes in gill samples of 13 individual shipworm specimens. Phylotype composition varied greatly; however, in all specimens the numerically dominant symbiont belonged to one of two nearly mutually exclusive phylotypes, each of which was detected with similar frequencies among specimens. A third phylotype, containing the culturable symbiont Teredinibacter turnerae , was identified in nearly all specimens, and two additional phylotypes were observed more sporadically. Such extensive variation in ribotype and phylotype composition among host specimens adds to a growing body of evidence that microbial endosymbiont populations may be both complex and dynamic and suggests that such genetic variation should be evaluated with regard to physiological and ecological differentiation.
- Published
- 2006
46. Surveying and harnessing the genetic, (meta)genomic, and metabolic potential of the deep carbonated biosphere
- Author
-
Janelle R.. Thompson., Massachusetts Institute of Technology. Department of Civil and Environmental Engineering., Freedman, Adam Joshua Ehrich, Janelle R.. Thompson., Massachusetts Institute of Technology. Department of Civil and Environmental Engineering., and Freedman, Adam Joshua Ehrich
- Abstract
Thesis: Ph. D. in Environmental Engineering, Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, 2016., Cataloged from PDF version of thesis., Includes bibliographical references (pages 165-190)., The interaction between microbes and supercritical (sc) carbon dioxide represents an increasingly compelling area of research due to use of scCO₂ in geologic carbon sequestration (GCS) and as a sustainable chemical solvent. To investigate the long-term effects of GCS on the in situ deep subsurface biosphere, I conducted a taxonomic, geochemical and metagenomic survey of the McElmo Dome sCCO₂ reservoir, which serves as a natural analog for GCS environments. Through 16S rRNA amplicon and metagenome sequencing, I identified Sulfurospirillum, Rhizobium, Desulfovibrio and members of the Clostridiales family associated with reservoir fluids. Annotations of complete genomes extracted from metagenomes predict diverse mechanisms for growth and nutrient cycling in deep subsurface sCCO₂ microbial ecosystems at McElmo Dome. Supercritical CO₂ is frequently used as a solvent for compound extraction and in vitro biocatalysis. However, due to its lethal effects, scCO₂ has previously been considered inaccessible for in vivo microbial bioproduct stripping. Utilizing a bioprospecting approach, I isolated strain Bacillus megaterium SR7 through enrichment culture and serial passaging of McElmo Dome scCO₂ reservoir fluids. I then initiated process improvements including media and culturing optimization under 1 atm CO₂ that increased SR7 growth frequency under scCO₂ . After developing a genetic system enabling inducible heterologous enzyme expression, scCO₂ incubations of SR7 transformed with a two-gene isobutanol biosynthesis pathway generated up to 93.5 mg/1 isobutanol. 5.2% of the total isobutanol was directly extracted by the scCO₂ headspace. This finding demonstrates for the first time the feasibility of active bioproduct synthesis and extraction in a single scCO₂-exposed bioreactor., by Adam Joshua Ehrich Freedman., Ph. D. in Environmental Engineering
- Published
- 2016
47. Diversity and Dynamics of a North Atlantic Coastal Vibrio Community
- Author
-
Martin F. Polz, Ee Lin Lim, Janelle R. Thompson, Mark A. Randa, Luisa A. Marcelino, and Aoy Tomita-Mitchell
- Subjects
Base Sequence ,Ecology ,biology ,Phylogenetic tree ,Molecular Sequence Data ,Electrophoresis, Capillary ,Ribosomal RNA ,biology.organism_classification ,16S ribosomal RNA ,Applied Microbiology and Biotechnology ,Vibrio ,Microbial Ecology ,Marine bacteriophage ,Vibrionaceae ,Abundance (ecology) ,Phylogenetics ,RNA, Ribosomal, 16S ,Water Microbiology ,Atlantic Ocean ,Phylogeny ,Food Science ,Biotechnology - Abstract
Vibrios are ubiquitous marine bacteria that have long served as models for heterotrophic processes and have received renewed attention because of the discovery of increasing numbers of facultatively pathogenic strains. Because the occurrence of specific vibrios has frequently been linked to the temperature, salinity, and nutrient status of water, we hypothesized that seasonal changes in coastal water bodies lead to distinct vibrio communities and sought to characterize their level of differentiation. A novel technique was used to quantify shifts in 16S rRNA gene abundance in samples from Barnegat Bay, N.J., collected over a 15-month period. Quantitative PCR (QPCR) with primers specific for the genus Vibrio was combined with separation and quantification of amplicons by constant denaturant capillary electrophoresis (CDCE). Vibrio populations identified by QPCR-CDCE varied between summer and winter samples, suggesting distinct warm-water and year-round populations. Identification of the CDCE populations by cloning and sequencing of 16S rRNA genes from two summer and two winter samples confirmed this distinction. It further showed that CDCE populations corresponded in most cases to ∼98% rRNA similarity groups and suggested that the abundance of these follows temperature trends. Phylogenetic comparison yielded closely related cultured and often pathogenic representatives for most sequences, and the temperature ranges of these isolates confirmed the trends seen in the environmental samples. Overall, this suggests that temperature is a good predictor of the occurrence of closely related vibrios but that considerable microdiversity of unknown significance coexists within this trend.
- Published
- 2004
48. Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by 'reconditioning PCR'
- Author
-
Martin F. Polz, Luisa A. Marcelino, and Janelle R. Thompson
- Subjects
DNA, Bacterial ,DNA Repair ,Sequence analysis ,Bacterial genome size ,Biology ,Polymerase Chain Reaction ,Article ,law.invention ,chemistry.chemical_compound ,law ,RNA, Ribosomal, 16S ,Genetics ,Polymerase chain reaction ,Vibrio ,Sequence (medicine) ,Cloning ,Genetic diversity ,Endodeoxyribonucleases ,Escherichia coli Proteins ,Nucleic Acid Heteroduplexes ,Electrophoresis, Capillary ,Genetic Variation ,DNA-Binding Proteins ,DNA Repair Enzymes ,chemistry ,Artifacts ,DNA ,Heteroduplex - Abstract
Although it has been recognized that PCR amplification of mixed templates may generate sequence artifacts, the mechanisms of their formation, frequency and potential elimination have not been fully elucidated. Here evidence is presented for heteroduplexes as a major source of artifacts in mixed-template PCR. Nearly equal proportions of homoduplexes and heteroduplexes were observed after co-amplifying 16S rDNA from three bacterial genomes and analyzing products by constant denaturing capillary electrophoresis (CDCE). Heteroduplexes became increasingly prevalent as primers became limiting and/or template diversity was increased. A model exploring the fate of cloned heteroduplexes during MutHLS-mediated mismatch repair in the Escherichia coli host demonstrates that the diversity of artifactual sequences increases exponentially with the number of both variable nucleotides and of original sequence variants. Our model illustrates how minimization of heteroduplex molecules before cloning may reduce artificial genetic diversity detected during sequence analysis by clone screening. Thus, we developed a method to eliminate heteroduplexes from mixed-template PCR products by subjecting them to ‘reconditioning PCR’, a low cycle number re-amplification of a 10-fold diluted mixed-template PCR product. This simple modification to the protocol may ensure that sequence richness encountered in clone libraries more closely reflects genetic diversity in the original sample.
- Published
- 2002
49. Microbes in the coral holobiont: partners through evolution, development, and ecological interactions
- Author
-
Janelle R. Thompson, Mónica Medina, Collin J. Closek, Hanny E. Rivera, Massachusetts Institute of Technology. Department of Civil and Environmental Engineering, Woods Hole Oceanographic Institution, Thompson, Janelle Renee, and Rivera, Hanny E.
- Subjects
0106 biological sciences ,Microbiology (medical) ,Ecology (disciplines) ,Coral ,Immunology ,lcsh:QR1-502 ,Context (language use) ,Review Article ,pollution and global change ,Bacterial Physiological Phenomena ,01 natural sciences ,Microbiology ,lcsh:Microbiology ,03 medical and health sciences ,Anthozoa ,Animals ,natural sciences ,14. Life underwater ,Microbiome ,Symbiosis ,coral ,holobiont ,030304 developmental biology ,ecosystem ,0303 health sciences ,geography ,geography.geographical_feature_category ,Bacteria ,biology ,metamorphosis ,Ecology ,010604 marine biology & hydrobiology ,fungi ,Metamorphosis, Biological ,technology, industry, and agriculture ,Bacterial interactions ,Coral reef ,biochemical phenomena, metabolism, and nutrition ,biology.organism_classification ,Biological Evolution ,Holobiont ,Infectious Diseases ,13. Climate action ,biological ,geographic locations ,Human Microbiome Project - Abstract
In the last two decades, genetic and genomic studies have revealed the astonishing diversity and ubiquity of microorganisms. Emergence and expansion of the human microbiome project has reshaped our thinking about how microbes control host health—not only as pathogens, but also as symbionts. In coral reef environments, scientists have begun to examine the role that microorganisms play in coral life history. Herein, we review the current literature on coral-microbe interactions within the context of their role in evolution, development, and ecology. We ask the following questions, first posed by McFall-Ngai et al. (2013) in their review of animal evolution, with specific attention to how coral-microbial interactions may be affected under future environmental conditions: (1) How do corals and their microbiome affect each other's genomes? (2) How does coral development depend on microbial partners? (3) How is homeostasis maintained between corals and their microbial symbionts? (4) How can ecological approaches deepen our understanding of the multiple levels of coral-microbial interactions? Elucidating the role that microorganisms play in the structure and function of the holobiont is essential for understanding how corals maintain homeostasis and acclimate to changing environmental conditions., Singapore-MIT Alliance for Research and Technology. Center for Environmental Sensing and Modeling, Massachusetts Institute of Technology. Department of Civil and Environmental Engineering, Massachusetts Institute of Technology. Presidential Fellowship
- Published
- 2014
50. Microbiota of the Major South Atlantic Reef Building Coral Mussismilia
- Author
-
Gizele D. Garcia, Jia Wang, Fabiano L. Thompson, Rodolfo Paranhos, Rodrigo L. de Moura, Kimberly M. Sparling, Janelle R. Thompson, Samodha C. Fernando, Ronaldo B. Francini-Filho, Massachusetts Institute of Technology. Department of Civil and Environmental Engineering, Fernando, Samodha C., Wang, Jia, Sparling, Kimberly M., and Thompson, Janelle Renee
- Subjects
DNA, Bacterial ,Coral ,Soil Science ,Microbial ecology ,Anthozoa ,RNA, Ribosomal, 16S ,Gammaproteobacteria ,Animals ,Cloning, Molecular ,Reef ,Ecology, Evolution, Behavior and Systematics ,Phylogeny ,Gene Library ,geography ,geography.geographical_feature_category ,Ecology ,biology ,Coral Reefs ,Microbiota ,fungi ,technology, industry, and agriculture ,Bacteroidetes ,Coral reef ,Sequence Analysis, DNA ,biochemical phenomena, metabolism, and nutrition ,biology.organism_classification ,Holobiont ,population characteristics ,Brazil ,geographic locations - Abstract
The Brazilian endemic scleractinian corals, genus Mussismilia, are among the main reef builders of the South Atlantic and are threatened by accelerating rates of disease. To better understand how holobiont microbial populations interact with corals during health and disease and to evaluate whether selective pressures in the holobiont or neutral assembly shape microbial composition, we have examined the microbiota structure of Mussismilia corals according to coral lineage, environment, and disease/health status. Microbiota of three Mussismilia species (Mussismilia harttii, Mussismilia hispida, and Mussismilia braziliensis) was compared using 16S rRNA pyrosequencing and clone library analysis of coral fragments. Analysis of biological triplicates per Mussismilia species and reef site allowed assessment of variability among Mussismilia species and between sites for M. braziliensis. From 173,487 V6 sequences, 6,733 coral- and 1,052 water-associated operational taxonomic units (OTUs) were observed. M. braziliensis microbiota was more similar across reefs than to other Mussismilia species microbiota from the same reef. Highly prevalent OTUs were more significantly structured by coral lineage and were enriched in Alpha- and Gammaproteobacteria. Bacterial OTUs from healthy corals were recovered from a M. braziliensis skeleton sample at twice the frequency of recovery from water or a diseased coral suggesting the skeleton is a significant habitat for microbial populations in the holobiont. Diseased corals were enriched with pathogens and opportunists (Vibrios, Bacteroidetes, Thalassomonas, and SRB). Our study examines for the first time intra- and inter-specific variability of microbiota across the genus Mussismilia. Changes in microbiota may be useful indicators of coral health and thus be a valuable tool for coral reef management and conservation., MIT International Science and Technology Initiatives (MIT-Brazil seed Grants Program), Conselho Nacional de Pesquisas (Brazil) (Grant), Carlos Chagas Filho Foundation for Research Support of the State of Rio de Janeiro, Brazil. Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (grant), United States. Embassy (grant), Massachusetts Institute of Technology. Center for Environmental Health Sciences
- Published
- 2014
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.