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Understanding human decomposition has the potential to significantly improve estimations of postmortem intervals (PMI), a key component of forensic investigations (1). The post-mortem interval is one of the most challenging pieces of evidence to obtain in the field of forensic science. In recent years, a novel approach for PMI calculations has emerged through the use of a microbial clock, an estimation tool based on microbial community data (2). This method, based on predictable patterns in microbial community progression, demonstrates that microbes provide an accurate clock starting at death and relies on the ecological changes in the microbial communities in the body and surrounding environment. However, there is not much known about how interactions between soil and the host microbiome influence PMI estimation. In the current study, we utilized specific pathogen free (SPF) and germ-free (GF) mice buried in non- sterile and sterile graves to identify sources of variability in microbial community progression. Intestinal and soil contents were collected over the course of a 21-day decomposition period and bacterial communities were identified by 16S sequencing. We found that GF mice remained sterile over the study period, regardless of soil sterility. In contrast, soil sterility did have an impact on microbial community dynamics in SPF mice. The data demonstrates that microbial communities at the time of death influence the entry of environmental microbes and microbial progression. Together, these results suggest that differences in the host microbiome at the time of death can significantly impact the predictive power of microbial succession in calculating PMI and should be taken into consideration when developing future models.

Sufu is a type of fermented food with abundant nutrients and delicious taste. It is made from the fermentation of tofu by various microorganisms. In this study, three types of sufu were prepared through natural fermentation: (NF), single‐strain fermentation (SF), and mixed‐strain fermentation (MF). Microbial species, amino acids, and fatty acids were identified to investigate dynamic changes in nutritional quality and microbial flora in sufu. The results showed that the number of microbial species in NF sufu was the highest (n = 284), whereas that in SF sufu was the lowest (n = 194). Overall, 153 microbial species were found in all three types of sufu. Relative abundance analysis also revealed that Tetragonococcus, Bacillus, Acinetobacter, and Staphylococcus were the main bacteria in sufu. However, there was a large number of harmful bacteria such as Enterococcaceae in NF sufu. The levels of various nutrients were low in SF sufu, whereas the contents of protein and soy isoflavones were higher in NF and MF sufu. Seventeen kinds of amino acids were detected, comprising seven essential amino acids and ten other amino acids. The contents of essential amino acids and essential fatty acids were higher in MF sufu than the other two types, resulting in its high nutritional value. The sufu produced through the three fermentation methods differed significantly (p, The microbial communities and nutrient contents in sufu were analyzed. There are differences in microbial community and nutrients in sufu. Sufu from a mixed fermentation had the best nutritional qualities.

Background: Diarrheagenic Escherichia coli (DEC) strains are predominant cause of gastrointestinal tract illnesses. The main objective of the study was to determine antibiotic resistance in various types of DEC isolated from chicken broilers farmed in Pakistan. Methods: A total of 200 feces and 200 meat samples from broiler chickens were collected from the slaughtering shops in Southern Punjab, Pakistan. The confirmed fecal (n=150) and meat (n=150) E. coli isolates were investigated against 16 antibiotics. Fourteen virulence genes specific for Enteropathogenic (EPEC), Shiga Toxin-producing (STEC), Enteroinvasive (EIEC), Enteroaggregative (EAEC), and Enterotoxigenic (ETEC) E. coli were identified using Polymerase Chain Reaction. Results: EPEC was the most detected pathotype in both feces (76%) and meat (90%) samples, followed by STEC, EIEC, and ETEC. The highest resistance (40-90%) was observed against penicillin, oxytetracycline, and nalidixic acid in fecal isolates. More than 50% EPEC and EAEC fecal isolates, and 60% EAEC meat isolates were simultaneously resistant to 6 or more antibiotics. Conclusion: Conclusively, the broiler meat sold in open markets of Pakistan was considerably contaminated with multi-drug resistant DEC. To mitigate the issue, the gov- ernment should regulate the use of antibiotics at poultry farms and monitor slaughtering practices in slaughterer houses.

In response to the spread of colistin resistance gene mcr-1, China banned the use of colistin in livestock fodders. We used a time-series analysis of inpatient colonization data from 2011-2019 to accurately reveal the associated fluctuations of mcr-1 that occurred in inpatients in response to the ban.

Staphylococcus aureus colonizes patients with atopic dermatitis (AD) and exacerbates disease by promoting inflammation. The present study investigated the safety and mechanisms of action of Staphylococcus hominis A9 (ShA9), a bacterium isolated from healthy human skin, as a topical therapy for AD. ShA9 killed S. aureus on the skin of mice and inhibited expression of a toxin from S. aureus (psmα) that promotes inflammation. A first-in-human, phase 1, double-blinded, randomized 1-week trial of topical ShA9 or vehicle on the forearm skin of 54 adults with S. aureus-positive AD (NCT03151148) met its primary endpoint of safety, and participants receiving ShA9 had fewer adverse events associated with AD. Eczema severity was not significantly different when evaluated in all participants treated with ShA9 but a significant decrease in S. aureus and increased ShA9 DNA were seen and met secondary endpoints. Some S. aureus strains on participants were not directly killed by ShA9, but expression of mRNA for psmα was inhibited in all strains. Improvement in local eczema severity was suggested by post-hoc analysis of participants with S. aureus directly killed by ShA9. These observations demonstrate the safety and potential benefits of bacteriotherapy for AD.

Masa is a traditionally fermented meal usually made from cereals. The aim of this research was to produce an enriched meal from rice and Bambara groundnut. The colour, functional properties and microbial quality of composite blend of rice and Bambara groundnut flour, in the ratio of 100:0, 95:5, 90:10, 85:15, 80:20, were evaluated using standard methods. Sensory properties of freshly made masa and masa prepared from stored flours were also determined. The microbial load of the masa flour blend increased over the storage period. Water absorption capacity, swelling capacity and bulk densities increased, while the oil absorption capacity decreased with the storage period. The objective colour result showed a decrease in the lightness (L*) value. Sensory properties of masa were not substantially altered with Bambara groundnut inclusion, but the ratings reduced with storage. Instant masa may be prepared from flour stored for 4 weeks without considerable changes in quality.

Background Much progress has been made in mapping genetic abnormalities linked to amyotrophic lateral sclerosis (ALS), but the majority of cases still present with no known underlying cause. Furthermore, even in families with a shared genetic abnormality there is significant phenotypic variability, suggesting that non-genetic elements may modify pathogenesis. Identification of such disease-modifiers is important as they might represent new therapeutic targets. A growing body of research has begun to shed light on the role played by the gut microbiome in health and disease with a number of studies linking abnormalities to ALS. Main body The microbiome refers to the genes belonging to the myriad different microorganisms that live within and upon us, collectively known as the microbiota. Most of these microbes are found in the intestines, where they play important roles in digestion and the generation of key metabolites including neurotransmitters. The gut microbiota is an important aspect of the environment in which our bodies operate and inter-individual differences may be key to explaining the different disease outcomes seen in ALS. Work has begun to investigate animal models of the disease, and the gut microbiomes of people living with ALS, revealing changes in the microbial communities of these groups. The current body of knowledge will be summarised in this review. Advances in microbiome sequencing methods will be highlighted, as their improved resolution now enables researchers to further explore differences at a functional level. Proposed mechanisms connecting the gut microbiome to neurodegeneration will also be considered, including direct effects via metabolites released into the host circulation and indirect effects on bioavailability of nutrients and even medications. Conclusion Profiling of the gut microbiome has the potential to add an environmental component to rapidly advancing studies of ALS genetics and move research a step further towards personalised medicine for this disease. Moreover, should compelling evidence of upstream neurotoxicity or neuroprotection initiated by gut microbiota emerge, modification of the microbiome will represent a potential new avenue for disease modifying therapies. For an intractable condition with few current therapeutic options, further research into the ALS microbiome is of crucial importance.

Background: Kebab is one of the popular ready-to-eat foods in Indonesia and sold as a street food. The purpose of this study was to determine occurrence and antibiotic resistance of Escherichia coli in street-vended kebab in Dramaga, Bogor, Indonesia. Methods: Totally, 43 samples of kebab meat were collected from street food kebab vendors. Examinations on Total Plate Count (TPC), and total E. coli using Most Probable Number (MPN) method were referred to the Indonesia National Standard. The antibiotic resistance test was carried out using the Kirby-Bauer disk diffusion method. Results: The mean of TPC in kebab samples was 5.3 log10 Colony Forming Unit (CFU)/g. Based on TPC, 13 out of 43 (30.2%) of kebab samples did not comply with the Indonesia National Standard with maximum acceptable level of 5 log10 CFU/g. E. coli was identified in 5 out of 43 samples (11.6%) with mean of 39.2 MPN/g ranged from 7.4 to 150 MPN/g which were higher than standard level (0.5 log10 CFU/g). Four out of 5 E. coli isolated from kebab samples were resistant to gentamycin. All E. coli isolates were susceptible to amoxicillin/clavulanate and chloramphenicol. Conclusion: The occurrence of antibiotic resistant E. coli in ready-to-eat kebab in this area of Indonesia could cause the health problem in consumers. The local government should conduct the monitoring and surveillance on the occurrence of pathogens and the antibiotic resistance in food chain.

Earthworms are important members of the soil macrofauna that play a significant role in soil structure and fertility. However, there is scanty information on the earthworm gut microbial flora and their metabolic potential. In the present study, the diversity of the microbial community and their metabolic potential from the gut content of four different earthworm species from Indo-Myanmar Biodiversity Hotspot were collected and identified by standard methods. The microbial diversity and their metabolic potential were assessed by high throughput sequencing of V3-V4 region of 16S rRNA using Illumina technology. Analysis of microbial diversity was performed by QIIME software package v.1.8.0 with their metabolic potential by PICRUSt (v1.1) software package. A total of 3,36,047 processed sequences were obtained that generated 3686 operational taxonomic units (OTUs). Major bacterial phyla identified were Proteobacteria (47.1%), Firmicutes (38.9%), Actinobacteria (6.3%), Bacteroidetes (3.6%) and Cyanobacteria (1.1%). The abundant genera were Lysinibacillus (26.9%), Acinetobacter (21.2%), Pseudomonas (4.7%), Bacillus (3.8%), Staphylococcus (3.5%), Stenotrophomonas (1.1%) and Ralstonia (1%). The functional annotation of the metagenome revealed abundance of bacterial community associated with amino acid, carbohydrate as well as energy metabolism. Furthermore, the presence of enzymes involved in the process of denitrification and methanogenesis were also identified. This study gives insight into the gut microbial composition and their putative functional roles in the gut of tropical hilly earthworms. The study on forest and garden soil earthworm gut microbiomes might help us understand the role of these organisms in their respective ecosystems.

Alpha-amylase reputes for starch modification by breaking of 1-4 glycosidic bands and is widely applied in different industrial sectors. Microorganisms express unique alpha-amylases with thermostable and halotolerant characteristics dependent on the microorganism’s intrinsic features. Likewise, genetic engineering methods are applied to produce enzymes with higher stability in contrast to wild types. As there are widespread application of α-amylase in industry, optimization methods like RSM are used to improve the production of the enzyme ex vivo. This study aimed to review the latest researches on the production improvement and stability of α-amylase.

The atypical trichromatic cyanobacterial phytochrome NpTP1 from Nostoc punctiforme ATCC 29133 is a linear tetrapyrrole (bilin)-binding photoreceptor protein that possesses tandem-cysteine residues responsible for shifting its light-sensing maximum to the violet spectral region. Using bioinformatics and phylogenetic analyses, here we established that tandem-cysteine cyanobacterial phytochromes (TCCPs) compose a well-supported monophyletic phytochrome lineage distinct from prototypical red/far-red cyanobacterial phytochromes. To investigate the light-sensing diversity of this family, we compared the spectroscopic properties of NpTP1 (here renamed NpTCCP) with those of three phylogenetically diverged TCCPs identified in the draft genomes of Tolypothrix sp. PCC7910, Scytonema sp. PCC10023, and Gloeocapsa sp. PCC7513. Recombinant photosensory core modules of ToTCCP, ScTCCP, and GlTCCP exhibited violet-blue-absorbing dark-states consistent with dual thioether-linked phycocyanobilin (PCB) chromophores. Photoexcitation generated singly-linked photoproduct mixtures with variable ratios of yellow-orange and red-absorbing species. The photoproduct ratio was strongly influenced by pH and by mutagenesis of TCCP- and phytochrome-specific signature residues. Our experiments support the conclusion that both photoproduct species possess protonated 15E bilin chromophores, but differ in the ionization state of the noncanonical "second" cysteine sulfhydryl group. We found that the ionization state of this and other residues influences subsequent conformational change and downstream signal transmission. We also show that tandem-cysteine phytochromes present in eukaryotes possess similar amino acid substitutions within their chromophore-binding pocket, which tune their spectral properties in an analogous fashion. Taken together, our findings provide a roadmap for tailoring the wavelength specificity of plant phytochromes to optimize plant performance in diverse natural and artificial light environments.

Alteration of antibiotic binding sites through modification of ribosomal RNA (rRNA) is a common form of resistance to ribosome-targeting antibiotics. The rRNA-modifying enzyme Cfr methylates an adenosine nucleotide within the peptidyl transferase center, resulting in the C-8 methylation of A2503 (m8A2503). Acquisition of cfr results in resistance to eight classes of ribosome-targeting antibiotics. Despite the prevalence of this resistance mechanism, it is poorly understood whether and how bacteria modulate Cfr methylation to adapt to antibiotic pressure. Moreover, direct evidence for how m8A2503 alters antibiotic binding sites within the ribosome is lacking. In this study, we performed directed evolution of Cfr under antibiotic selection to generate Cfr variants that confer increased resistance by enhancing methylation of A2503 in cells. Increased rRNA methylation is achieved by improved expression and stability of Cfr through transcriptional and post-transcriptional mechanisms, which may be exploited by pathogens under antibiotic stress as suggested by natural isolates. Using a variant that achieves near-stoichiometric methylation of rRNA, we determined a 2.2 Å cryo-electron microscopy structure of the Cfr-modified ribosome. Our structure reveals the molecular basis for broad resistance to antibiotics and will inform the design of new antibiotics that overcome resistance mediated by Cfr., eLife digest Antibiotics treat or prevent infections by killing bacteria or slowing down their growth. A large proportion of these drugs do this by disrupting an essential piece of cellular machinery called the ribosome which the bacteria need to make proteins. However, over the course of the treatment, some bacteria may gain genetic alterations that allow them to resist the effects of the antibiotic. Antibiotic resistance is a major threat to global health, and understanding how it emerges and spreads is an important area of research. Recent studies have discovered populations of resistant bacteria carrying a gene for a protein named chloramphenicol-florfenicol resistance, or Cfr for short. Cfr inserts a small modification in to the ribosome that prevents antibiotics from inhibiting the production of proteins, making them ineffective against the infection. To date, Cfr has been found to cause resistance to eight different classes of antibiotics. Identifying which mutations enhance its activity and protect bacteria is vital for designing strategies that fight antibiotic resistance. To investigate how the gene for Cfr could mutate and make bacteria more resistant, Tsai et al. performed a laboratory technique called directed evolution, a cyclic process which mimics natural selection. Genetic changes were randomly introduced in the gene for the Cfr protein and bacteria carrying these mutations were treated with tiamulin, an antibiotic rendered ineffective by the modification Cfr introduces into the ribosome. Bacteria that survived were then selected and had more mutations inserted. By repeating this process several times, Tsai et al. identified ‘super’ variants of the Cfr protein that lead to greater resistance. The experiments showed that these variants boosted resistance by increasing the proportion of ribosomes that contained the protective modification. This process was facilitated by mutations that enabled higher levels of Cfr protein to accumulate in the cell. In addition, the current study allowed, for the first time, direct visualization of how the Cfr modification disrupts the effect antibiotics have on the ribosome. These findings will make it easier for clinics to look out for bacteria that carry these ‘super’ resistant mutations. They could also help researchers design a new generation of antibiotics that can overcome resistance caused by the Cfr protein.

Food safety is a global phenomenon. The public has become more concerned about the risks from food hazards in recent years. This study was carried out to evaluate polycyclic aromatic hydrocarbon profiles, microbial safety and heavy metal concentrations of smoke-dried grass cutter meat samples purchased from different processing and marketing centers in Osun State, Nigeria. A total of 60 smoke-dried grass cutter meat samples were randomly collected between February and April, 2019. Smoke-dried grass cutter meat samples purchased from different processing and marketing centers were analyzed to determine polycyclic aromatic hydrocarbon profile, microbial safety and heavy metal concentrations. The results revealed existence of significant differences (P ≤ 0.05) between polycyclic aromatic hydrocarbon profile, microbial safety and heavy metal concentrations of smoke-dried grass cutter meat samples purchased from different processing and marketing centers. The concentrations of carcinogenic PAHs, acenaphthene (Acy), fluorine (Fln), 1,2-Benzanthracene (1,2-BAnt), phenanthrene, pyrene (Pyr), anthracene (Ant), fluoranthene (Flan), benzo[a]anthracene (B[a]A), chrysene, benzo[b]fluoranthene (B[b]FA), benzo[a]pyrene (B[a]P), benzo[ghi]perylene (B[ghi]P) and indeno[1,2,3-cd]anthracene (ID[1,2,3-cd]A) in smoke-dried grass cutter meat samples from different processing and marketing centers exceeded the maximum limit of 2 μgkg−1 of B[a]P in meat products approved by European Commission regulations (EU) No. 1881/2006 and 835/2011. In this study, Escherichia coli, Salmonella paratyphi, Listeria monocytogenes and Campylobacter jejuni were detected in all the samples analyzed. In all cases, the presence of Escherichia coli, Salmonella paratyphi, Listeria monocytogenes and Campylobacter jejuni suggests poor manufacturing practices and fecal contamination of the products as Salmonella paratyphi and Escherichia coli serve as indicator organisms for fecal contamination of foods. The values of the heavy metals obtained in the study were generally below the maximum acceptable limits set by World Health Organization for Pb (0.3 ppm), Hg (0.2 ppm), As (0.2 ppm), Cd (0.2 ppm) and Cr (0.5 ppm) and hence pose no risk to consumers.

Natural evolution has produced an almost infinite variety of microorganisms that can colonize almost any conceivable habitat. Since the vast majority of these microbial consortia are still unknown, there is a great need to elucidate this “microbial dark matter” (MDM) to enable exploitation in biotechnology. We report the fabrication and application of a novel device that integrates a matrix of macroporous elastomeric silicone foam (MESIF) into an easily fabricated and scalable chip design that can be used for decoding MDM in environmental microbiomes. Technical validation, performed with the model organism Escherichia coli expressing a fluorescent protein, showed that this low-cost, bioinert, and widely modifiable chip is rapidly colonized by microorganisms. The biological potential of the chip was then illustrated through targeted sampling and enrichment of microbiomes in a variety of habitats ranging from wet, turbulent moving bed biofilters and wastewater treatment plants to dry air-based environments. Sequencing analyses consistently showed that MESIF chips are not only suitable for sampling with high robustness but also that the material can be used to detect a broad cross section of microorganisms present in the habitat in a short time span of a few days. For example, results from the biofilter habitat showed efficient enrichment of microorganisms belonging to the enigmatic Candidate Phyla Radiation, which comprise ∼70% of the MDM. From dry air, the MESIF chip was able to enrich a variety of members of Actinobacteriota, which is known to produce specific secondary metabolites. Targeted sampling from a wastewater treatment plant where the herbicide glyphosate was added to the chip’s reservoir resulted in enrichment of Cyanobacteria and Desulfobacteria, previously associated with glyphosate degradation. These initial case studies suggest that this chip is very well suited for the systematic study of MDM and opens opportunities for the cultivation of previously unculturable microorganisms.

Anthropogenic impacts on freshwater ecosystems cause critical losses of biodiversity that can in turn impair key processes such as decomposition and nutrient cycling. Forest streams are mainly subsidized by terrestrial organic detritus, so their functioning and conservation status can be altered by changes in forest biodiversity and composition, particularly if these changes involve the replacement of functional groups or the loss of key species. We examined this issue using a microcosm experiment where we manipulated plant functional diversity (FD) (monocultures and low-FD and high-FD mixtures, resulting from different combinations of deciduous and evergreen Quercus species) and the presence of a key species (Alnus glutinosa), all in presence and absence of detritivores, and assessed effects on litter decomposition, nutrient cycling, and fungal and detritivore biomass. We found (i) positive diversity effects on detritivore-mediated decomposition, litter nutrient losses and detritivore biomass exclusively when A. glutinosa was present; and (ii) negative effects on the same processes when microbially mediated and on fungal biomass. Most positive trends could be explained by the higher litter palatability and litter trait variability obtained with the inclusion of alder leaves in the mixture. Our results support the hypothesis of a consistent slowing down of the decomposition process as a result of plant biodiversity loss, and hence effects on stream ecosystem functioning, especially when a key (N-fixing) species is lost; and underscore the importance of detritivores as drivers of plant diversity effects in the studied ecosystem processes. This study was funded by the 2014–2020 FEDER Operative Program Andalusia (RIOVEGEST project, Ref. FEDER-UAL18 -RNM -B006 – B, to J.J.C). Additional support was provided by the Spanish Ministry for Science, Innovation and Universities and FEDER (BioLoss project, Ref. RTI2018-095023- B-I00, to L.B.). Rubio-Ríos was supported by an FPU grant of the Spanish Ministry of Education, Culture and Sports (reference FPU16/03734).

Understanding the molecular determinants underlying the interaction between the leaf and human pathogenic bacteria is key to provide the foundation to develop science-based strategies to prevent or decrease the pathogen contamination of leafy greens. In this study, we conducted a dual RNA-sequencing analysis to simultaneously define changes in the transcriptomic profiles of the plant and the bacterium when they come in contact. We used an economically relevant vegetable crop, lettuce (Lactuca sativa L. cultivar Salinas), and a model plant, Arabidopsis thaliana Col-0, as well as two pathogenic bacterial strains that cause disease outbreaks associated with fresh produce, Escherichia coli O157:H7 and Salmonella enterica serovar Typhimurium 14028s (STm 14028s). We observed commonalities and specificities in the modulation of biological processes between Arabidopsis and lettuce and between O157:H7 and STm 14028s during early stages of the interaction. We detected a larger alteration of gene expression at the whole transcriptome level in lettuce and Arabidopsis at 24 h post inoculation with STm 14028s compared to that with O157:H7. In addition, bacterial transcriptomic adjustments were substantially larger in Arabidopsis than in lettuce. Bacterial transcriptome was affected at a larger extent in the first 4 h compared to the subsequent 20 h after inoculation. Overall, we gained valuable knowledge about the responses and counter-responses of both bacterial pathogen and plant host when these bacteria are residing in the leaf intercellular space. These findings and the public genomic resources generated in this study are valuable for additional data mining.

The endoplasmic reticulum (ER) is an essential organelle in cells that synthesizes, folds and modifies membrane and secretory proteins. It has a crucial role in cell survival and growth, thus requiring strict control of its quality and homeostasis. Autophagy of the ER fragments, termed ER-phagy or reticulophagy, is an essential mechanism responsible for ER quality control. It transports stress-damaged ER fragments as cargo into the lysosome for degradation to eliminate unfolded or misfolded protein aggregates and membrane lipids. ER-phagy can also function as a host defense mechanism when pathogens infect cells, and its deficiency facilitates viral infection. This review briefly describes the process and regulatory mechanisms of ER-phagy, and its function in host anti-microbial defense during infection.

The COVID-19 pandemic, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is considered the greatest challenge to the global health community of the century as it continues to expand. This has prompted immediate urgency to discover promising drug targets for the treatment of COVID-19. The SARS-CoV-2 viral proteases, 3-chymotrypsin-like protease (3CLpro) and papain-like cysteine protease (PLpro), have become the promising target to study due to their essential functions in spreading the virus by RNA transcription, translation, protein synthesis, processing and modification, virus replication, and infection of the host. As such, understanding of the structure and function of these two proteases is unavoidable as platforms for the development of inhibitors targeting this protein which further arrest the infection and spread of the virus. While the abundance of reports on the screening of natural compounds such as SARS-CoV-2 proteases inhibitors are available, the microorganisms-based compounds (peptides and non-peptides) remain less studied. Indeed, microorganisms-based compounds are also one of the potent antiviral candidates against COVID-19. Microbes, especially bacteria and fungi, are other resources to produce new drugs as well as nucleosides, nucleotides, and nucleic acids. Thus, we have compiled various reported literature in detail on the structures, functions of the SARS-CoV-2 proteases, and potential inhibitors from microbial sources as assistance to other researchers working with COVID-19. The compounds are also compared to HIV protease inhibitors which suggested the microorganisms-based compounds are advantageous as SARS-CoV2 proteases inhibitors. The information should serve as a platform for further development of COVID-19 drug design strategies.

Background Advances in microbiome science are being driven in large part due to our ability to study and infer microbial ecology from genomes reconstructed from mixed microbial communities using metagenomics and single-cell genomics. Such omics-based techniques allow us to read genomic blueprints of microorganisms, decipher their functional capacities and activities, and reconstruct their roles in biogeochemical processes. Currently available tools for analyses of genomic data can annotate and depict metabolic functions to some extent; however, no standardized approaches are currently available for the comprehensive characterization of metabolic predictions, metabolite exchanges, microbial interactions, and microbial contributions to biogeochemical cycling. Results We present METABOLIC (METabolic And BiogeOchemistry anaLyses In miCrobes), a scalable software to advance microbial ecology and biogeochemistry studies using genomes at the resolution of individual organisms and/or microbial communities. The genome-scale workflow includes annotation of microbial genomes, motif validation of biochemically validated conserved protein residues, metabolic pathway analyses, and calculation of contributions to individual biogeochemical transformations and cycles. The community-scale workflow supplements genome-scale analyses with determination of genome abundance in the microbiome, potential microbial metabolic handoffs and metabolite exchange, reconstruction of functional networks, and determination of microbial contributions to biogeochemical cycles. METABOLIC can take input genomes from isolates, metagenome-assembled genomes, or single-cell genomes. Results are presented in the form of tables for metabolism and a variety of visualizations including biogeochemical cycling potential, representation of sequential metabolic transformations, community-scale microbial functional networks using a newly defined metric “MW-score” (metabolic weight score), and metabolic Sankey diagrams. METABOLIC takes ~ 3 h with 40 CPU threads to process ~ 100 genomes and corresponding metagenomic reads within which the most compute-demanding part of hmmsearch takes ~ 45 min, while it takes ~ 5 h to complete hmmsearch for ~ 3600 genomes. Tests of accuracy, robustness, and consistency suggest METABOLIC provides better performance compared to other software and online servers. To highlight the utility and versatility of METABOLIC, we demonstrate its capabilities on diverse metagenomic datasets from the marine subsurface, terrestrial subsurface, meadow soil, deep sea, freshwater lakes, wastewater, and the human gut. Conclusion METABOLIC enables the consistent and reproducible study of microbial community ecology and biogeochemistry using a foundation of genome-informed microbial metabolism, and will advance the integration of uncultivated organisms into metabolic and biogeochemical models. METABOLIC is written in Perl and R and is freely available under GPLv3 at https://github.com/AnantharamanLab/METABOLIC.

The objective of this study is to identify and analyze integrons and antibiotic resistance genes (ARGs) in samples collected from diverse sites in terrestrial Antarctica. Integrons were studied using two independent methods. One involved the construction and analysis of intI gene amplicon libraries. In addition, we sequenced 17 metagenomes of microbial mats and soil by high‐throughput sequencing and analyzed these data using the IntegronFinder program. As expected, the metagenomic analysis allowed for the identification of novel predicted intI integrases and gene cassettes (GCs), which mostly encode unknown functions. However, some intI genes are similar to sequences previously identified by amplicon library analysis in soil samples collected from non‐Antarctic sites. ARGs were analyzed in the metagenomes using ABRIcate with CARD database and verified if these genes could be classified as GCs by IntegronFinder. We identified 53 ARGs in 15 metagenomes, but only four were classified as GCs, one in MTG12 metagenome (Continental Antarctica), encoding an aminoglycoside‐modifying enzyme (AAC(6´)acetyltransferase) and the other three in CS1 metagenome (Maritime Antarctica). One of these genes encodes a class D β‐lactamase (blaOXA‐205) and the other two are located in the same contig. One is part of a gene encoding the first 76 amino acids of aminoglycoside adenyltransferase (aadA6), and the other is a qacG2 gene., The objective of this study is to identify and analyze integrons and antibiotic resistance genes (ARGs) in samples collected from diverse sites in terrestrial Antarctica. The metagenomic analysis allowed us to identify novel predicted intI integrases and gene cassettes (GCs), which mostly encode unknown functions.

Plant parasitic nematodes are a major problem for growers worldwide, causing severe crop losses. Several conventional strategies, such as chemical nematicides and biofumigation, have been employed in the past to manage their infection in plants and spread in soils. However, the search for the most sustainable and environmentally safe practices is still ongoing. This review summarises information on plant parasitic nematodes, their distribution, and their interaction with their host plants, along with various approaches to manage their infestations. It also focuses on the application of microbial and fermentation-based bionematicides that have not only been successful in controlling nematode infection but have also led to plant growth promotion and proven to be environmentally safe. Studies with new information on the relative abundance of plant parasitic nematodes in two agricultural sites in the Republic of Ireland are also reported. This review, with the information it provides, will help to generate an up-to-date knowledge base on plant parasitic nematodes and their management practices.

Background: Food contamination with Listeria spp. can occur at all stages of the food chain. The aim of this research was to investigate the prevalence, molecular identification, antimicrobial resistance, and disinfectant susceptibility of Listeria innocua isolated from Ready-To-Eat (RTE) foods sold in Johannesburg, South Africa. Methods: Eighty RTE foods were collected from Johannesburg, South Africa. The 16S rRNA region of L. innocua isolates was amplified, sequenced, and identified using Basic Alignment Search Tool (BLAST). The antimicrobial resistance and disinfectant susceptibility (against four commercial disinfectants) of the isolates were evaluated using disk diffusion and microdilution assays. Data were statistically analyzed using SPSS v. 23.0. Results: Listeria strains revealed a high 16S rRNA gene sequence analogy to L. innocua of between 98-99%. The overall prevalence of L. innocua was 21.3% (17 out of 80) in the RTE food samples. Most isolates were susceptible to the studied commercial disinfectants. All the L. innocua isolates from food sources were found to be resistant to ampicillin and cephalothin, while 83 and 74% of isolates were resistant to colistin sulphate and sulphatriad. Conclusion: Prevalence of L. innocua was considerable in the RTE food samples sold in Johannesburg, South Africa. The L. innocua isolates showed high antibiotic resistance against ampicillin, cephalothin, colistin sulphate, and sulphatriad.

Background: When animal manures are used, food products may include pathogenic bacteria, especially Escherichia coli. The major aim of the current study was to investigate TEM (blaTEM) and SHV beta-lactamase (blaSHV) genes in E. coli isolated from strawberry samples in Sanandaj, Iran. Methods: In this study, 150 strawberry samples were collected from farms (traditional), greenhouses, and packages in Sanandaj, Iran. E. coli contamination was done using routine culture methods. Then, isolates were investigated for Extended-Spectrum Beta-Lactamase (ESBL) production and blaTEM or blaSHV genes using phenotypic and genotypic methods, respectively. Results: The most susceptibility and resistance of E. coli to antibiotics were related to chloramphenicol and trimethoprim/sulfamethoxazole, respectively. Out of 21 isolates of E. coli, eight were resistant to ceftazidime and cefotaxime; from which, six isolates were ESBL-producer. Furthermore, Polymerase Chain Reaction (PCR) analysis of six ESBL- producing E. coli isolates showed that four isolates included blaTEM gene, while no isolates included blaSHV gene. Conclusion: In this study, multiple antibiotic resistance patterns were seen in E. coli isolates, especially ESBL patterns in E. coli isolated from strawberries produced in Iran.

This work was supported by the grants obtained by M.P-C: (FPU 15/04284; "Formacion de Profesorado Universitario") and EST 18/00610 ("Ayudas a la movilidad para estancias breves y traslados temporales") from Spanish Ministry (Ministerio de Universidades) . Funding was also provided by grants CGL2014-59616-R; RTI2018.101548.B.I00 to M.L. M. Funding for open access charge: University of Granada/CBUA. The authors thank Concepcion Hernandez-Castillo and Maria del Mar Abad Ortega for their assistance with microscopy at the University of Granada ("Centro de Instrumentacion Cientifica") . We also thank Dr. Kenneth McCreath for editorial support., The widespread use of selenium (Se) in technological applications (e.g., solar cells and electronic devices) has led to an accumulation of this metalloid in the environment to toxic levels. The newly described bacterial strain Stenotrophomonas bentonitica BII-R7 has been demonstrated to reduce mobile Se(IV) to Se(0)-nanoparticles (Se(0) NPs) and volatile species. Amorphous Se-nanospheres are reported to aggregate to form crystalline nanostructures and trigonal selenium. We investigated the molecular mechanisms underlying the biotransformation of Se(IV) to less toxic forms using differential shotgun proteomics analysis of S. bentonitica BII-R7 grown with or without sodium selenite for three different time-points. Results showed an increase in the abundance of several proteins involved in Se(IV) reduction and stabilization of Se(0)NPs, such as glutathione reductase, in bacteria grown with Se(IV), in addition to many proteins with transport functions, including RND (resistance-nodulationdivision) systems, possibly facilitating Se uptake. Notably proteins involved in oxidative stress defense (e.g., catalase/peroxidase HPI) were also induced by Se exposure. Electron microscopy analyses confirmed the biotransformation of amorphous nanospheres to trigonal Se. Overall, our results highlight the potential of S. bentonitica in reducing the bioavailability of Se, which provides a basis both for the development of bioremediation strategies and the eco-friendly synthesis of biotechnological nanomaterials., Spanish Ministry (Ministerio de Universidades) FPU 15/04284 EST 18/00610, University of Granada/CBUA, CGL2014-59616-R RTI2018.101548

Antimicrobial resistance is a growing problem threatening human health. Inappropriate antibiotic use is the main driver of the growing development and spread of antimicrobial resistance, but may al...

Background & objective Carbapenem-resistant Enterobacteriaceae is a growing concern worldwide including Iran. The emergence of this pathogen is worrying as carbapenem is one of the 'last-line' antibiotics for treatment of infections caused by multi drug resistant gram- negative bacteria. The main objective of this study was to determine the prevalence of carbapenem-resistant Enterobacteriaceae in a referral hospital in Tehran, Iran. Methods In this study, all positive isolates of Enterobacteriaceae recorded in blood, urine, and other body fluids were studied during April 2017 to April 2018 in a referral hospital in Tehran. All cases of resistance to carbapenems were first tested by modified Hodge test. All cases with positive or negative test, after gene extraction, were examined genotypically based on the primers designed for the three Klebsiella pneumoniae carbapenemase (KPC), New Delhi metallo-β-lactamase (NDM), and OXA-48 genes by conventional PCR method. Results 108 isolates (13.6%) were resistant to all cephalosporins as well as to imipenem and meropenem. In a genotypic study, including 45 isolates, 13 isolates were positive for OXA-48 gene, 11 isolates for OXA-48 and NDM genes, 11 isolates for OXA-48, NDM and KPC genes, 4 isolates for OXA-48 genes and KPC, 3 isolates for NDM, one isolate for KPC. On the other hand, two isolates were negative for all three genes examined. Conclusion OXA-48 gene was one of the most common genes resistant to carbapenems in Iran. According to studies, the prevalence of antibiotic resistance in Iran is rising dramatically, which reduces the choice of antibiotics to treat severe infections in the future.

Preservation of fossil fuels are currently depleting with the massive exploitation of fuels. In this condition, breakthroughs are necessary to produce alternative fuels. One of the breakthroughs is bioethanol. It is a renewable energy which is more effective than gasoline inasmuch it can increase combustion efficiency and reduce exhaust emissions. In this work, a bioethanol process was done by using sugarcane bagasse waste material which has a lot of lignin and cellulose content. The content was converted into bioethanol by utilizing a strong base to degrade lignin and T. Viride as cellulose-producing and S. cereviseae yeast as a sugar converter to bioethanol. This present research aims to find the best formula of bioethanol production based on sugarcane bagasse with variations in cellulose hydrolysis temperature, shaking speed, and fermentation time by using an integrated shaker machine fuzzy-logic control of temperature and humidity. This research employed a complete randomized design experimental research (CRD) to test temperature, speed, and time modification by using a shaker machine. The independent variables were: (1) temperature, (2) shaking speed, and (3) fermentation time. The dependent variables measured were reducing sugar and bioethanol levels. The results showed that the best formula for producing bioethanol levels was at a treatment temperature of 45 °C and a speed of 140 rpm with fermentation time of 48 hours which resulted in a bioethanol level of 2.75%.

Background: In Ayurveda, metal-based preparations, that is Bhasma (incinerated Rasaushadhi), are indicated for the treatment of several diseases. Trivanga Bhasma is a classical Ayurvedic preparation containing Bhasmas of three metals, namely Vanga (Tin), Naga (Lead), and Yashada (zinc), and it is indicated in Madhumeha (diabetes) and MutraRoga (urinary disorders), Napunasakta (impotency), Vandhyatva (Infertility), Swetapradara (Leucorrhea), Vata-Pittadosa, and as Shaktivardhaka(strength). Aims: The study was carried out the stability of Kumari Swarasa Bhavita Trivanga Bhasma concerning its microbial profile. Materials and Methods: A sample of Kumari Swarasa Bhavita Trivanga Bhasma was prepared and studied to check microbial contamination at regular intervals. Results: Every time, the sample was subjected to the microbiological study from the date of the preparation to the date of the last microbiological study. No contamination was found in the microbiological study. Discussion: Hence, the present study was carried out to observe the stability study of Kumari Swarasa Bhavita Trivanga Bhasma concerning microbial contamination of the sample prepared and preserved in different climatic and temperature conditions. Thus, a baseline microbial profile was studied at regular intervals. At the end of the study, it was found that the sample was not shown the presence of any microbes. Conclusion: In the microbiological study of Kumari Swarasa Bhavita Trivanga Bhasma, there was no growth found of microorganisms (bacterial or fungal), from the date of preparation, shown shelf life for 296 days. Hence, in the present study, the stability test of Kumari Swarasa Bhavita Trivanga Bhasma concerning microbiological findings was negative at room temperature, warm and cold, dry, and humid conditions.

Different metacommunity perspectives have been developed to describe the relationship between environmental and spatial factors and their relative roles for local communities. However, only little is known about temporal variation in metacommunities and their underlying drivers. We examined temporal variation in the relative roles of environmental and spatial factors for diatom community composition among brackish-watered rock pools on the Baltic Sea coast over a 3-month period. We used a combination of direct ordination, variation partition, and Mantel tests to investigate the metacommunity patterns. The studied communities housed a mixture of freshwater, brackish, and marine species, with a decreasing share of salinity tolerant species along both temporal and spatial gradients. The community composition was explained by both environmental and spatial variables (especially conductivity and distance from the sea) in each month; the joint effect of these factors was consistently larger than the pure effects of either variable group. Community similarity was related to both environmental and spatial distance between the pools even when the other variable group was controlled for. The relative influence of environmental factors increased with time, accounting for the largest share of the variation in species composition and distance decay of similarity in July. Metacommunity organization in the studied rock pools was probably largely explained by a combination of species sorting and mass effect given the small spatial study scale. The found strong distance decay of community similarity indicates spatially highly heterogeneous diatom communities mainly driven by temporally varying conductivity gradient at the marine-freshwater transition zone.

Background Antibiotic-resistant (AR) bacteria are a global threat. AR bacteria can be acquired in early life and have long-term sequelae. Limiting the spread of antibiotic resistance without triggering the development of additional resistance mechanisms is of immense clinical value. Here, we show how the infant gut microbiome can be modified, resulting in a significant reduction of AR genes (ARGs) and the potentially pathogenic bacteria that harbor them. Methods The gut microbiome was characterized using shotgun metagenomics of fecal samples from two groups of healthy, term breastfed infants. One group was fed B. infantis EVC001 in addition to receiving lactation support (n = 29, EVC001-fed), while the other received lactation support alone (n = 31, controls). Coliforms were isolated from fecal samples and genome sequenced, as well as tested for minimal inhibitory concentrations against clinically relevant antibiotics. Results Infants fed B. infantis EVC001 exhibited a change to the gut microbiome, resulting in a 90% lower level of ARGs compared to controls. ARGs that differed significantly between groups were predicted to confer resistance to beta lactams, fluoroquinolones, or multiple drug classes, the majority of which belonged to Escherichia, Clostridium, and Staphylococcus. Minimal inhibitory concentration assays confirmed the resistance phenotypes among isolates with these genes. Notably, we found extended-spectrum beta lactamases among healthy, vaginally delivered breastfed infants who had never been exposed to antibiotics. Conclusions Colonization of the gut of breastfed infants by a single strain of B. longum subsp. infantis had a profound impact on the fecal metagenome, including a reduction in ARGs. This highlights the importance of developing novel approaches to limit the spread of these genes among clinically relevant bacteria. Future studies are needed to determine whether colonization with B. infantis EVC001 decreases the incidence of AR infections in breastfed infants. Trial registration This clinical trial was registered at ClinicalTrials.gov, NCT02457338. Electronic supplementary material The online version of this article (10.1186/s13756-019-0583-6) contains supplementary material, which is available to authorized users.

We engaged metagenomic next generation sequencing to longitudinally assess the gut microbiota and antimicrobial resistomes of international travelers to understand global exchange of resistant organisms. Travel resulted in an increase in antimicrobial resistance genes and a greater proportion ofEscherichiaspecies within gut microbial communities without impacting diversity.

Background: Muscle foods, notably red meat, poultry meat, and fish are the first choice of animal source food with adequate protein for human. The present study was undertaken to analyze the load and antibiotic susceptibility pattern of microorganisms in muscle foods sold in Akure, Southwest Nigeria. Methods: Hundred muscle food samples, including meat and fish were collected from different locations (A-E) of Akure, Nigeria and examined microbiologically using cultural techniques, biochemical tests, and analytical profile index. Antibiotic susceptibility patterns were also determined in isolated microorganisms from muscle foods against different antibiotics. Data were analyzed using SPSS software version 17.0. Results: The highest (p

International audience; This study combined culture-dependent (strain isolation plus molecular identification) and culture-independent (metabarcoding) approaches to characterize the diversity of microbiota on wheat and oilseed rape residues. The goal was to develop a methodology to culture microorganisms with the aim of being able to establish synthetic crop residue microbial communities for further study, i.e., testing potential interactions within these communities and characterizing groups of beneficial taxa that could be used as biological control agents against plant pathogens. We generated community-based culture collections. We adapted the isolation strategy to the potential differences in the spatial and temporal distribution of diversity between bacteria and fungi. We performed (i) a high-throughput isolation from few samples with no a priori for bacteria and (ii) a low-throughput isolation from several samples with a priori—i.e., morphotype selection—for fungi. Although isolation using a single medium did not allow us to characterize the microbiome as precisely as metabarcoding, the bacterial diversity (158 ASVs, 36 genera) was relatively higher than the fungal diversity (131 ASVs, 17 genera) known to be limited by competition for growth on non-selective solid media. Isolation and metabarcoding provided consistent and complementary information: they revealed several common but also specific ASVs, leading to close microbial community profiles of the most abundant fungal and bacterial taxa in residues. Finally, by empirically comparing the different profiles, we assessed the cultivability of the most abundant fungal and bacterial taxa obtained in metabarcoding.

Microbial communities are frequently numerically dominated by just a few species. Often, the long “tail” of the rank-abundance plots of microbial communities constitutes the so-called “rare biosphere,” microorganisms that are highly diverse but are typically found in low abundance in these communities. Their presence in microbial communities has only recently become apparent with advances in high-throughput sequencing technologies. Despite their low numbers, they are thought to play important roles in their communities and may function as potential members to keep the communities intact and resilient. Their phylogenetic diversity also means that they are important subjects for better understanding the interplay between microbial diversity and evolution. I propose that more efforts should be put into characterizing these poorly understood and mostly unknown microbial lineages that hold vast potentials for our understanding of microbial diversity, ecology, and evolution of life on this planet.

Terrestrial ecosystems are an important carbon store, and this carbon is vulnerable to microbial degradation with climate warming. After 30 years of experimental warming, carbon stocks in a temperate mixed deciduous forest were observed to be reduced by 30% in the heated plots relative to the controls. In addition, soil respiration was seasonal, as was the warming treatment effect. We therefore hypothesized that long-term warming will have higher expressions of genes related to carbohydrate and lipid metabolism due to increased utilization of recalcitrant carbon pools compared to controls. Because of the seasonal effect of soil respiration and the warming treatment, we further hypothesized that these patterns will be seasonal. We used RNA sequencing to show how the microbial community responds to long-term warming (~30 years) in Harvard Forest, MA. Total RNA was extracted from mineral and organic soil types from two treatment plots (+5°C heated and ambient control), at two time points (June and October) and sequenced using Illumina NextSeq technology. Treatment had a larger effect size on KEGG annotated transcripts than on CAZymes, while soil types more strongly affected CAZymes than KEGG annotated transcripts, though effect sizes overall were small. Although, warming showed a small effect on overall CAZymes expression, several carbohydrate-associated enzymes showed increased expression in heated soils (~68% of all differentially expressed transcripts). Further, exploratory analysis using an unconstrained method showed increased abundances of enzymes related to polysaccharide and lipid metabolism and decomposition in heated soils. Compared to long-term warming, we detected a relatively small effect of seasonal variation on community gene expression. Together, these results indicate that the higher carbohydrate degrading potential of bacteria in heated plots can possibly accelerate a self-reinforcing carbon cycle-temperature feedback in a warming climate.

According to the characteristics of aniline dyeing wastewater, aerobic biological treatment was adopted herein, and high-throughput sequencing technology was used to analyze the changes to the microbial community structure and diversity in the aerobic sludge acclimation stage. As a result, according to the experimental study on the effects of different biomass, the initial pH value and the salinity with the aerobic biological treatment, the chemical oxygen demand (COD) degradation rate can increase linearly with the increase in biomass under different biomass conditions. The organic matter degradation rate is 6.24 mg/L COD·h−1·(mg/L·MLSS)−1, with a correlation coefficient (R2) of 0.98704. When the initial pH value is less than 7.0 ± 0.2, the COD degradation rate increases with the increase in the initial pH value and then decreases gradually. The optimal sludge concentration is 4 g/L, the optimal initial pH value is in the range of 7.0–8.0, the optimal salinity is 1.7%. When the initial concentration of COD is 3000 mg/L, the COD value gradually stabilizes and decreases to 1500 mg/L after 32 h, the degradation rate reaches 50%, and the pH decreases from 7.5 to 4.5. Sphingopyxis has been detected in sludge samples from the third cycle of acclimation, which can biodegrade aromatic compounds, anthraquinone dyes, and their intermediates, and the relative abundance of Sphingopyxis increased from 0.18% to 5.08%, indicating a potential biodegradation ability of aniline dyeing wastewater.

Metagenomics facilitates the study of the genetic information from uncultured microbes and complex microbial communities. Assembling complete genomes from metagenomics data is difficult because most samples have high organismal complexity and strain diversity. Some studies have attempted to extract complete bacterial, archaeal, and viral genomes and often focus on species with circular genomes so they can help confirm completeness with circularity. However, less than 100 circularized bacterial and archaeal genomes have been assembled and published from metagenomics data despite the thousands of datasets that are available. Circularized genomes are important for (1) building a reference collection as scaffolds for future assemblies, (2) providing complete gene content of a genome, (3) confirming little or no contamination of a genome, (4) studying the genomic context and synteny of genes, and (5) linking protein coding genes to ribosomal RNA genes to aid metabolic inference in 16S rRNA gene sequencing studies. We developed a semi-automated method called Jorg to help circularize small bacterial, archaeal, and viral genomes using iterative assembly, binning, and read mapping. In addition, this method exposes potential misassemblies from k-mer based assemblies. We chose species of the Candidate Phyla Radiation (CPR) to focus our initial efforts because they have small genomes and are only known to have one ribosomal RNA operon. In addition to 34 circular CPR genomes, we present one circular Margulisbacteria genome, one circular Chloroflexi genome, and two circular megaphage genomes from 19 public and published datasets. We demonstrate findings that would likely be difficult without circularizing genomes, including that ribosomal genes are likely not operonic in the majority of CPR, and that some CPR harbor diverged forms of RNase P RNA. Code and a tutorial for this method is available at https://github.com/lmlui/Jorg and is available on the DOE Systems Biology KnowledgeBase as a beta app., Author summary Since we cannot culture many microorganisms that are found in the environment, animals, and the human body, scientists rely on shotgun metagenomics to reveal their genomes and to infer their traits and capabilities. However, shotgun metagenomics often only provides fragmented genomes due to limitations of available sequencing technology and bioinformatics tools. We present a semi-automated method called Jorg that can be used to improve and eventually complete (i.e., circular with no misassemblies) prokaryotic and viral genomes from short read metagenomics data, and also include quality checks for misassemblies and completeness. As a proof-of-concept we circularized 36 bacterial genomes and two megaphage genomes. For comparison, there are only ~100 known circularized bacterial genomes from metagenomes from ~30 other studies. We also demonstrate findings that illustrate the utility of circularizing genomes by discovering new biological patterns in Candidate Phyla Radiation species. High-quality circularized genomes produced using this tool also can be used as scaffolds to improve future genome assemblies and as data to improve identification of species in microbiomes.

Background To investigate the trends and correlation between antibacterial consumption and carbapenem resistance in Gram-negative bacteria from 2012 to 2019 in a tertiary-care teaching hospital in southern China. Methods This retrospective study included data from hospital-wide inpatients collected between January 2012 and December 2019. Data on antibacterial consumption were expressed as defined daily doses (DDDs)/1000 patient-days. Antibacterials were classified according to the Anatomical Therapeutic Chemical (ATC) classification system. The trends in antimicrobial usage and resistance were analyzed by linear regression, while Pearson correlation analysis was used for assessing correlations. Results An increasing trend in the annual consumption of tetracyclines, β-lactam/β-lactamase inhibitor (BL/BLI) combinations, and carbapenems was observed (P Acinetobacter baumannii (A. baumannii) significantly increased (P A. baumannii (P Escherichia coli (E. coli; P A. baumannii to carbapenems was positively correlated with cephalosporin/β-lactamase inhibitor (C/BLI) combinations (P P Burkholderia cepacia (B. cepacia) to carbapenems (P P P Enterobacter cloacae (E. cloacae) to carbapenems. Conclusion These results revealed significant correlations between consumption of antibiotics and carbapenem resistance rates in Gram-negative bacteria. Implementing proper management strategies and reducing the unreasonable use of antibacterial drugs may be an effective measure to reduce the spread of carbapenem-resistant Gram-negative bacteria (CRGN), which should be confirmed by further studies.

This project was funded by SCK CEN (Belgium) through the PhD project of Tom Rogiers., Cupriavidus metallidurans is a model bacterium to study molecular metal resistance mechanisms and its use for the bioremediation of several metals has been shown. However, its mechanisms for radionuclide resistance are unexplored. We investigated the interaction with uranium and associated cellular response to uranium for Cupriavidus metallidurans NA4. Strain NA4 actively captured 98 ± 1% of the uranium in its biomass after growing 24 h in the presence of 100 μM uranyl nitrate. TEM HAADF-EDX microscopy confirmed intracellular uraniumphosphate precipitates that were mainly associated with polyhydroxybutyrate. Furthermore, whole transcriptome sequencing indicated a complex transcriptional response with upregulation of genes encoding general stress-related proteins and several genes involved in metal resistance. More in particular, gene clusters known to be involved in copper and silver resistance were differentially expressed. This study provides further insights into bacterial interactions with and their response to uranium. Our results could be promising for uranium bioremediation purposes with the multi-metal resistant bacterium C. metallidurans NA4., SCK CEN (Belgium)

Significance Light-driven rhodopsin proteins pump ions across cell membranes. They have applications in optogenetics and can potentially be used to develop solar energy–harvesting devices. A detailed understanding of rhodopsin dynamics and functions may therefore assist research in medicine, health, and clean energy. This time-resolved crystallography study carried out with X-ray free-electron lasers reveals detailed dynamics of chloride ion–pumping rhodopsin (ClR) within 100 ps of light activation. It shows the dissociation of Cl− from the Schiff base binding site upon light-triggered retinal isomerization. This Cl− dissociation is followed by diffusion toward the intracellular direction. The results hint at a common ion-pumping mechanism across rhodopsin families., Chloride ion–pumping rhodopsin (ClR) in some marine bacteria utilizes light energy to actively transport Cl− into cells. How the ClR initiates the transport is elusive. Here, we show the dynamics of ion transport observed with time-resolved serial femtosecond (fs) crystallography using the Linac Coherent Light Source. X-ray pulses captured structural changes in ClR upon flash illumination with a 550 nm fs-pumping laser. High-resolution structures for five time points (dark to 100 ps after flashing) reveal complex and coordinated dynamics comprising retinal isomerization, water molecule rearrangement, and conformational changes of various residues. Combining data from time-resolved spectroscopy experiments and molecular dynamics simulations, this study reveals that the chloride ion close to the Schiff base undergoes a dissociation–diffusion process upon light-triggered retinal isomerization.

Drought is one of the main abiotic stresses that cause crop yield loss. Improving crop yield under drought stress is a major goal of crop breeding, as it is critical to food security. The mechanism of plant drought resistance has been well studied, and diverse drought resistance genes have been identified in recent years, but transferring this knowledge from the laboratory to field production remains a significant challenge. Recently, some new strategies have become research frontiers owing to their advantages of low cost, convenience, strong field operability, and/or environmental friendliness. Exogenous plant growth regulator (PGR) treatment and microbe-based plant biotechnology have been used to effectively improve crop drought tolerance and preserve yield under drought stress. However, our understanding of the mechanisms by which PGRs regulate plant drought resistance and of plant-microbiome interactions under drought is still incomplete. In this review, we summarize these two strategies reported in recent studies, focusing on the mechanisms by which these exogenous treatments regulate crop drought resistance. Finally, future challenges and directions in crop drought resistance breeding are discussed., Over the past few years, a variety of new strategies have been devised to improve crop tolerance to drought stress. This review summarizes studies on the use of exogenous plant growth regulators (PGRs) and microorganism inoculation to improve crop drought resistance, focusing on the regulatory mechanisms by which these exogenous treatments influence crop drought resilience.

Liver transplant recipients are at high risk for surgical site infections (SSIs). Limited data are available on SSI epidemiology following liver transplant procedures (LTPs). We analyzed data on SSIs from 2015 to 2018 reported to CDC's National Healthcare Safety Network to determine rates, pathogen distribution, and antimicrobial resistance after LTPs and other hepatic, biliary, or pancreatic procedures (BILIs). LTP and BILI SSI rates were 5.7% and 5.9%, respectively. The odds of SSI after LTP were lower than after BILI (adjusted odds ratio = 0.70, 95% confidence interval 0.57‐0.85). Among LTP SSIs, 43.1% were caused by Enterococcus spp., 17.2% by Candida spp., and 15.0% by coagulase‐negative Staphylococcus spp. (CNS). Percentages of SSIs caused by Enterococcus faecium or CNS were higher after LTPs than BILIs, whereas percentages of SSIs caused by Enterobacteriaceae, Enterococcus faecalis, or viridans streptococci were higher after BILIs. Antimicrobial resistance was common in LTP SSI pathogens, including E. faecium (69.4% vancomycin resistant); Escherichia coli (68.8% fluoroquinolone non‐susceptible and 44.7% extended spectrum cephalosporin [ESC] non‐susceptible); and Klebsiella pneumoniae and K. oxytoca (39.4% fluoroquinolone non‐susceptible and 54.5% ESC non‐susceptible). National LTP SSI pathogen and resistance data can help prioritize studies to determine effective interventions to prevent SSIs and reduce antimicrobial resistance in liver transplant recipients.

Oregano (Origanum vulgare L.) and thyme (Thymus vulgaris L.) have long been known for their organoleptic properties. Both plants are widely used in cuisine worldwide in fresh and dried form and as a pharmaceutical raw material. The study aimed to assess if the type of cultivation influenced chosen chemical parameters (total polyphenols by Folin-Ciocalteu method, carotenoids and chlorophyll content by Lichtenthaler method), antimicrobial activity (with chosen reference microbial strains) and shaped cytotoxicity (with L929 mouse fibroblasts cell line) in water macerates of dry oregano and thyme. Polyphenols content and antimicrobial activity were higher in water macerates obtained from conventional cultivation (independently from herb species), unlike the pigments in a higher amount in macerates from organic herbs cultivation. Among all tested macerates stronger antimicrobial properties (effective in inhibiting the growth of Pseudomonas aeruginosa, Bacillus cereus and Salmonella enteritidis) and higher cytotoxicity (abilities to diminish the growth of L929 fibroblasts cytotoxicity) characterized the conventionally cultivated thyme macerate.

Profiles of symbiotic microbial communities (“microbiomes”) can provide insight into the natural history and ecology of their hosts. Using high throughput DNA sequencing of the 16S rRNA V4 region, microbiomes of five shark species in South Florida (nurse, lemon, sandbar, Caribbean reef, and tiger) have been characterized for the first time. The microbiomes show species specific microbiome composition, distinct from surrounding seawater. Shark anatomical location (gills, teeth, skin, cloaca) affected the diversity of microbiomes. An in-depth analysis of teeth communities revealed species specific microbial communities. For example, the genus Haemophilus, explained 7.0% of the differences of the teeth microbiomes of lemon and Caribbean reef sharks. Lemon shark teeth communities (n = 11) contained a high abundance of both Vibrio (10.8 ± 26.0%) and Corynebacterium (1.6 ± 5.1%), genera that can include human pathogenic taxa. The Vibrio (2.8 ± 6.34%) and Kordia (3.1 ± 6.0%) genera and Salmonella enterica (2.6 ± 6.4%) were the most abundant members of nurse shark teeth microbial communities. The Vibrio genus was highly represented in the sandbar shark (54.0 ± 46.0%) and tiger shark (5.8 ± 12.3%) teeth microbiomes. The prevalence of genera containing potential human pathogens could be informative in shark bite treatment protocols and future research to confirm or deny human pathogenicity. We conclude that South Florida sharks host species specific microbiomes that are distinct from their surrounding environment and vary due to differences in microbial community composition among shark species and diversity and composition among anatomical locations. Additionally, when considering the confounding effects of both species and location, microbial community diversity and composition varies.

Our understanding of human microbial communities, in particular in regard to diseases is advancing, yet the basic understanding of the microbiome in healthy subjects over time remains limited. The oropharynx is a key target for colonization by several important human pathogens. To understand how the oropharyngeal microbiome might limit infections, and how intercurrent infections might be associated with its composition, we characterized the oropharyngeal microbiome of 18 healthy adults, sampled weekly over a 40-weeks using culture-independent molecular techniques. We detected nine phyla, 202 genera and 1438 assignments on OTU level, dominated by Firmicutes, Bacteroidetes, and Proteobacteria on phylum level. Individual microbiomes of participants were characterized by levels of high alpha diversity (mean = 204.55 OTUs, sd = 35.64), evenness (19.83, sd = 9.74) and high temporal stability (mean Pearson’s correlation between samples of 0.52, sd = 0.060), with greater differences in microbiome community composition between than within individuals. Significant changes in community composition were associated with disease states, suggesting that it is possible to detect specific changes in OTU abundance and community composition during illness. We defined the common core microbiota by varying occurrence and abundance thresholds showing that individual core microbiomes share a substantial number of OTUs across participants, chiefly Streptococci and Veillonella. Our results provide insights into the microbial communities that characterize the healthy human oropharynx, community structure and variability, and provide new approaches to define individual and shared cores. The wider implications of this result include the potential for modeling the general dynamics of oropharynx microbiota both in health and in response to antimicrobial treatments or probiotics.

Background: Tuber aestivum Vittad., known as black summer truffle, represents high-value food especially used as garnishment in nouvelle cuisine. The aim of this study was to investigate on the viable microbial populations associated with T. aestivum ascomata collected in different sites of Sicily and one locality of Umbria (Italy). Methods: The ripe ascomata of black summer truffles were collected from Central Italy. Cell densities of spoilage bacteria, fecal indicators, potential pathogens, yeasts, and molds were analyzed. Statistical analysis was conducted with XLSTAT software. Results: The microbiological counts of truffles ranged between 6.00 and 9.63 log Colony Forming Unit (CFU)/g for total mesophilic count and between 6.18 and 8.55 log CFU/g for total psychrotrophic count; pseudomonads were in the range 6.98-9.28 log CFU/g. Listeria spp. and coagulase-positive streptococci detected in no samples. Coagulase-negative streptococci were found in some samples with 2.11-4.76 log CFU/g levels. Yeasts and filamentous fungi were detected at consistent levels of 3.60-7.81 log CFU/g. Significant differences (p

Antibiotic resistance genes (ARGs) are emerging contaminants causing serious global health concern. Interventions to address this concern include improving our understanding of methods for treating waste material of human and animal origin that are known to harbor ARGs. Anaerobic digestion is a commonly used process for treating dairy manure, and although effective in reducing ARGs, its mechanism of action is not clear. In this study, we used three ARGs to conducted a longitudinal bench scale anaerobic digestion experiment with various temperatures (28, 36, 44, and 52°C) in triplicate using fresh dairy manure for 30 days to evaluate the reduction of gene abundance. Three ARGs and two mobile genetic elements (MGEs) were studied: sulfonamide resistance gene (sulII), tetracycline resistance genes (tetW), macrolide-lincosamide-streptogramin B (MLSB) superfamily resistance genes (ermF), class 1 integrase gene (intI1), and transposase gene (tnpA). Genes were quantified by real-time quantitative PCR. Results show that the thermophilic anaerobic digestion (52°C) significantly reduced (p < 0.05) the absolute abundance of sulII (95%), intI1 (95%), tnpA (77%) and 16S rRNA gene (76%) after 30 days of digestion. A modified Collins–Selleck model was used to fit the decay curve, and results suggest that the gene reduction during the startup phase of anaerobic digestion (first 5 days) was faster than the later stage, and reductions in the first five days were more than 50% for most genes.