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Abstract Dysbiosis of the gut-liver axis increases the risk of bacterial and metabolite influx into the liver, which may contribute to the development of hepatocellular carcinoma (HCC). In this study, we compared the microbiomes in HCC tumors and adjacent tissues. We examined the HCC tumors and adjacent tissues from 19 patients diagnosed with HCC. We find that the liver tissues from HCC patients with capsule invasion presented higher alpha diversity at the genus level than those without. The bacterial compositions in liver tissues of HCC patients at stage II differed from those at stage I and Advanced, respectively. Metagenomic profiling revealed that order Actinomycetales was enriched in the HCC patients at advanced stages. Order Lactobacillales, family Veillonellaceae, genera Rhodobacter and Megasphaera are enriched in tumors of HCC patients, whereas genus Pseudochrobactrum is enriched in the adjacent tissues from HCC patients. An increased abundance of class Actinobacteria and order Actinomycetales is observed in the HCC patients with cirrhosis. In contrast, phylum Firmicutes, classes Clostridia and Betaproteobacteria, and order Clostridiales are enriched in those without cirrhosis. The presence of various types of bacterial 16S rRNAs in HCC tumors and adjacent tissues indicates the presence of various bacterial communities therein. Our study provides information about differentially abundant intrahepatic bacteria in patients with HCC. The differences found may support possible diagnostic and personalized therapeutic implications for HCC.

Background: Biofilm formation on implant-abutment surfaces can cause inflammatory reactions. Ethical concerns often limit intraoral testing, necessitating preliminary in vitro or animal studies. Here, we propose an in vitro model using human saliva and hypothesize that this model has the potential to closely mimic the dynamics of biofilm formation on implant-abutment material surfaces in vivo. Methods: A saliva stock was mixed with modified Brain-Heart-Infusion medium to form biofilms on Titanium-Aluminum-Vanadium (Ti6Al4V) and Yttria-partially Stabilized Zirconia (Y-TZP) discs in 24-well plates. Biofilm analyses included crystal violet staining, intact cell quantification with BactoBox, 16S rRNA gene analysis, and short-chain fatty acids measurement. As a control, discs were worn in maxillary splints by four subjects for four days to induce in vivo biofilm formation. Results: After four days, biofilms fully covered Ti6Al4V and Y-TZP discs both in vivo and in vitro, with similar cell viability. There was a 60.31% overlap of genera between invitro and invivo biofilms in the early stages, and 41% in the late stages. Ten key oral bacteria, including Streptococcus, Haemophilus, Neisseria, Veillonella, and Porphyromonas, were still detectable in vitro, representing the common stages of oral biofilm formation. Conclusion: This invitro model effectively simulates oral conditions and provides valuable insights into biofilm dynamics. [ABSTRACT FROM AUTHOR]

Dysbiosis of the gut-liver axis increases the risk of bacterial and metabolite influx into the liver, which may contribute to the development of hepatocellular carcinoma (HCC). In this study, we compared the microbiomes in HCC tumors and adjacent tissues. We examined the HCC tumors and adjacent tissues from 19 patients diagnosed with HCC. We find that the liver tissues from HCC patients with capsule invasion presented higher alpha diversity at the genus level than those without. The bacterial compositions in liver tissues of HCC patients at stage II differed from those at stage I and Advanced, respectively. Metagenomic profiling revealed that order Actinomycetales was enriched in the HCC patients at advanced stages. Order Lactobacillales, family Veillonellaceae, genera Rhodobacter and Megasphaera are enriched in tumors of HCC patients, whereas genus Pseudochrobactrum is enriched in the adjacent tissues from HCC patients. An increased abundance of class Actinobacteria and order Actinomycetales is observed in the HCC patients with cirrhosis. In contrast, phylum Firmicutes, classes Clostridia and Betaproteobacteria, and order Clostridiales are enriched in those without cirrhosis. The presence of various types of bacterial 16S rRNAs in HCC tumors and adjacent tissues indicates the presence of various bacterial communities therein. Our study provides information about differentially abundant intrahepatic bacteria in patients with HCC. The differences found may support possible diagnostic and personalized therapeutic implications for HCC. [ABSTRACT FROM AUTHOR]

Objectives: To determine the characteristics of the endodontic microbiome. Material and Methods: Saliva, plaque, and infected root canal wall dentin of two teeth suffering from apical periodontitis were harvested from a 58‐year‐old man. Bacterial DNA was extracted from each sample, and 16S rRNA gene analysis targeting the V3–V4 region was conducted on the Illumina MiSeq platform using QIIME2. The functional potential of the microbiomes was inferred using PICRUSt2. Results: The four microbiomes were different in structure and membership, yet the nine most abundant metabolic pathways were common among them. The two endodontic microbiomes were more anaerobic, rich in Firmicutes, and scarce in Actinobacteriota and Proteobacteria, compared with saliva and plaque microbiomes. Their profiles were dissimilar despite their clinical and radiographic similarities. Conclusions: The endodontic microbiomes were anaerobic, rich in Firmicutes, scarce in Actinobacteriota and Proteobacteria, and considerably varied within an individual. [ABSTRACT FROM AUTHOR]

Abstract Objectives To determine the characteristics of the endodontic microbiome. Material and Methods Saliva, plaque, and infected root canal wall dentin of two teeth suffering from apical periodontitis were harvested from a 58‐year‐old man. Bacterial DNA was extracted from each sample, and 16S rRNA gene analysis targeting the V3–V4 region was conducted on the Illumina MiSeq platform using QIIME2. The functional potential of the microbiomes was inferred using PICRUSt2. Results The four microbiomes were different in structure and membership, yet the nine most abundant metabolic pathways were common among them. The two endodontic microbiomes were more anaerobic, rich in Firmicutes, and scarce in Actinobacteriota and Proteobacteria, compared with saliva and plaque microbiomes. Their profiles were dissimilar despite their clinical and radiographic similarities. Conclusions The endodontic microbiomes were anaerobic, rich in Firmicutes, scarce in Actinobacteriota and Proteobacteria, and considerably varied within an individual.

Rivers are the main route for plastic entering the ocean, including the Musi River Estuary. Characteristics of bacteria that are able to degrade plastic waste through polymerase enzymes. The aim of this research is to determine the ability of bacterial isolates to degrade plastic and identify the types of bacteria that degrade plastic waste. This study used plastic bottles, nylon nets, and snack wrappers as objects for degradation measurement. Identification analysis of the 16S rRNA gene using universal PCR primers for bacteria in the form of forward primer 63f (5'-CAG GCC TAA CAC ATG CAA GTC-3') and reverse primer 1387r (5'-GGG CGG WGT GTA CAA GGC-3'). The type of bacteria with the highest percentage of degradation over 20 days, amounting to 7.75%, was Bacillus amyloliquefaciens. Identification of types of plastic degrading bacteria using 16S rRNA gene analysis showed 11 bacteria with 8 types including Staphylococcus hominis, Pseudomonas aeruginosa, Acinetobacter sp., Acinetobacter baumannii, Acinetobacter variabilis, Shewanella sp., Micrococcus luteus, and Bacillus amyloliquefaciens. The percentage of plastic degradation by bacteria is relatively small, so it is best to look for times where there is potential for bacterial growth. [ABSTRACT FROM AUTHOR]

While microbial communities in limestone caves across the world are relatively understood, knowledge of the microbial composition in lava tubes is lagging behind. These caves are found in volcanic regions worldwide and are typically lined with multicolored microbial mats on their walls and ceilings. The Mount Etna (Sicily, S-Italy) represents one of the most active volcanos in the world. Due to its outstanding biodiversity and geological features, it was declared Natural Heritage of Humanity by the UNESCO in 2013. Despite the presence of more than 200 basaltic lava tubes, the microbial diversity of these hypogean systems has never been investigated so far. Here, we investigated bacterial communities in four lava tubes of Mount Etna volcano. Field emission scanning electron microscopy (FESEM) was carried out for the morphological characterization and detection of microbial features. We documented an abundant presence of microbial cells with different morphotypes including rod-shaped, filamentous, and coccoidal cells with surface appendages, resembling actinobacteria reported in other lava tubes across the world. Based on 16S rRNA gene analysis, the colored microbial mats collected were mostly composed of bacteria belonging to the phyla Actinomycetota, Pseudomonadota, Acidobacteriota, Chloroflexota, and Cyanobacteria. At the genus level, the analysis revealed a dominance of the genus Crossiella, which is actively involved in biomineralization processes, followed by Pseudomonas, Bacillus, Chujaibacter, and Sphingomonas. The presence of these taxa is associated with the carbon, nitrogen, and ammonia cycles, and some are possibly related to the anthropic disturbance of these caves. This study provides the first insight into the microbial diversity of the Etna volcano lava tubes, and expands on previous research on microbiology of volcanic caves across the world. [ABSTRACT FROM AUTHOR]

Constructed Wetlands (CWs) are a cost-effective, versatile and sustainable choice for wastewater treatment. In these environments, microbial communities play a significant role in pollutant removal. However, little is known about how microbial communities in full-scale CWs contribute to maintaining water quality or how their dynamics change in response to pulse disturbances such as fire or freezes. Furthermore, few studies have examined the relationship between CW microbial community structure and performance in full-scale industrial operations. We characterized the water-column and leaf-litter layer microbial communities in a 110-acre free water surface CW that provides tertiary wastewater treatment to a plastics manufacturing plant. The CW’s sampling campaign was conducted over a 12-month period that included Winter Storm Uri, a 100-year freeze event. Analysis of 16S rRNA gene amplicon sequences revealed that the bacterial communities experienced a temporal shift. There was also a shift in microbial community structure between the influent and the first segment of the CW. However, no differences in microbial community structure were observed in the second segment of the CW. There was a negative association between microbial community diversity and chlorophyll a, as well as microbial community diversity and total suspended solids (TSS); demonstrating an increase in microbial biodiversity as water quality improved throughout the CW. Six months after the freeze, CW performance in terms of removal of water quality constituents began to return to former removal trends. Yet, there was still a significant difference in microbial community structure within the CW relative to the previous year. This suggests CW functional resilience despite a shift in microbial community structure in the wetland.

Methane seeps are highly abundant marine habitats that contribute sources of chemosynthetic primary production to marine ecosystems. Seeps also factor into the global budget of methane, a potent greenhouse gas. Because of these factors, methane seeps influence not only local ocean ecology, but also biogeochemical cycles on a greater scale. Methane seeps host specialized microbial communities that vary significantly based on geography, seep gross morphology, biogeochemistry, and a diversity of other ecological factors including cross-domain species interactions. In this study, we collected sediment cores from six seep and non-seep locations from Grays and Quinault Canyons (46–47°N) off Washington State, USA, as well as one non-seep site off the coast of Oregon, USA (45°N) to quantify the scale of seep influence on biodiversity within marine habitats. These samples were profiled using 16S rRNA gene sequencing. Predicted gene functions were generated using the program PICRUSt2, and the community composition and predicted functions were compared among samples. The microbial communities at seeps varied by seep morphology and habitat, whereas the microbial communities at non-seep sites varied by water depth. Microbial community composition and predicted gene function clearly transitioned from on-seep to off-seep in samples collected from transects moving away from seeps, with a clear ecotone and high diversity where methane-fueled habitats transition into the non-seep deep sea. Our work demonstrates the microbial and metabolic sphere of influence that extends outwards from methane seep habitats. [ABSTRACT FROM AUTHOR]

Bacteria are an essential biotic component in freshwater environments. A group of 262 bacterial strains of freshwater environments from an altitudinal gradient in the Eastern Cordillera of Colombia was identified using the 16S rRNA gene sequence analysis. Hill numbers and related diversity indices were calculated to know the bacteria diversity in this collection and environments. In addition, the Bray–Curtis index was also calculated to know the differences in genera composition between sampled localities and their relationship with altitudinal gradient. The identified bacterial strains were grouped into 7 major phylogenetic groups (Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Flavobacteriia, Actinomycetes, Clostridia, and Bacilli), 38 genera, and 84 distinctive species. Diversity analysis based on Hill numbers showed that the diversity concerning bacteria inhabiting freshwater environments was consistently high. Dominant genera were Klebsiella, Serratia , and Pseudomonas , although other genera such as Bacillus, Lelliottia , and Obesumbacterium were well represented per locality. The highest bacterial diversity came from localities Cimitarra and El Carmen del Chucurí, while those originating from Santa Bárbara and Páramo del Almorzadero were relatively lower diverse. Differences in diversity were found to be mainly due to the spatial replacement of one genus by another and, to a lesser extent, to the loss or gain of taxa. [ABSTRACT FROM AUTHOR]

We report the case of a 77-year-old Japanese woman with neuromyelitis optica spectrum disorder treated with 15 mg of prednisolone daily who presented with acute septic shock and altered consciousness due to Dolosigranulum pigrum bacteremia. Intravenous fluid and broad-spectrum antibiotics were initiated; however, the patient died shortly after admission. We performed 16S rRNA sequencing and analyzed the murJ gene. A phylogenetic tree constructed using the neighbor-joining method showed that the strain belonged to Clade C3, according to the Flores Ramos classification system. Although D. pigrum is a commensal of the upper respiratory tract and is rarely associated with infections, it can occasionally cause serious infections. Further clinical and bacteriological data are needed to provide an understanding of the pathogenicity and infections caused by this organism.

Methane seeps are highly abundant marine habitats that contribute sources of chemosynthetic primary production to marine ecosystems. Seeps also factor into the global budget of methane, a potent greenhouse gas. Because of these factors, methane seeps influence not only local ocean ecology, but also biogeochemical cycles on a greater scale. Methane seeps host specialized microbial communities that vary significantly based on geography, seep gross morphology, biogeochemistry, and a diversity of other ecological factors including cross-domain species interactions. In this study, we collected sediment cores from six seep and non-seep locations from Grays and Quinault Canyons (46–47°N) off Washington State, USA, as well as one non-seep site off the coast of Oregon, USA (45°N) to quantify the scale of seep influence on biodiversity within marine habitats. These samples were profiled using 16S rRNA gene sequencing. Predicted gene functions were generated using the program PICRUSt2, and the community composition and predicted functions were compared among samples. The microbial communities at seeps varied by seep morphology and habitat, whereas the microbial communities at non-seep sites varied by water depth. Microbial community composition and predicted gene function clearly transitioned from on-seep to off-seep in samples collected from transects moving away from seeps, with a clear ecotone and high diversity where methane-fueled habitats transition into the non-seep deep sea. Our work demonstrates the microbial and metabolic sphere of influence that extends outwards from methane seep habitats.

The work studied the methanogenic microbial consortium in a coal mine from the Bogotá basin in Colombia. Ex situ coal-enrichment cultures were established for in vitro growth and de novo gas production. Biogenic gas produced by cultures was analyzed by gas chromatography using thermal conductivity and flame ionization detectors. Cultures were used to isolate microbial specimens and to generate 16S rRNA gene libraries employing bacterial and archaeal primer sets. The gas chromatographic analysis showed methane production at 37 oC, but not at 60 oC, where CO2 was the major component of the biogenic gas. 16S rRNA gene sequence analysis of microbial isolates and clone libraries established that the methanogenic microbial consortium was formed by bacteria species from Bacillus and Gracilibacter genera plus archaea from the Methanothermobacter genus. This methanogenic microbial consortium was potentially responsible for biogenic gas generation in La Ciscuda coal mine. The results suggested that these methanogens produced methane by hydrogenotrophic or CO2 reduction pathways.

Copyright of Revista Colombiana de Biotecnología is the property of Universidad Nacional de Colombia and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Purpose: To evaluate the efficacy of identifying the bacteria by aqueous sampling and vitreous sampling in postoperative infectious endophthalmitis using 16S ribosomal RNA (rRNA) gene analysis with a nanopore sequencer (MinION™). Observation: A 55-year-old woman who underwent cataract surgery at an ophthalmology clinic 18 days ago was referred to our hospital for suspected endophthalmitis. She had light perception visual acuity in her right eye; however, the eye was severely inflamed, with a hypopyon and a fibrinous membrane in the anterior chamber. The fundus was not visible because of vitreous opacity on a B-scan image. Based on the diagnosis of postoperative acute infectious endophthalmitis, we performed a vitrectomy, intraocular lens extraction, and silicone oil tamponade. On postoperative day 14, the inflammation resolved. An aqueous sample was collected before surgical treatment, and the vitreous sample was collected during the operation. Both samples underwent 16S rRNA gene analysis with a nanopore sequencer MinION™ to identify the causative organism. Conclusions and Importance: In the aqueous humor, Granulicatella adiacens and Cutibacterium acnes were identified before the operation, while only Granulicatella adiacens was detected in the vitreous sample after the operation. Although the aqueous humor sample might contain commensal bacteria, it could provide a predictable result before the operation. It can also provide a substitute for a vitreous sample to allow earlier identification of the causative organism.

Aim Wound infection is a life-threatening complication of pressure injuries (PIs) and is not yet completely preventable. This study aims to explore the dissemination of microbiota between PIs and hospital beds using a culture-independent methodology. This serves as the first step towards developing a new intervention to prevent wound infection. Methods A cross-sectional study was conducted at a longterm care hospital on patients aged >65 years with PIs. The microbiota of wounds, skin and beds were identified using 16S ribosomal RNA (rRNA) gene sequencing analysis. Zero-radius operational taxonomic units (zOTUs) were used for confirming dissemination which indicates bacteria possessing identical sequences within the V3-V4 region of the 16S rRNA gene. Results Ten PIs were analysed in this study. All individuals had zOTUs common to samples from their wound, skin and bed (median: 194, interquartile range [IQR]: 121-320). Furthermore, the bed samples were classified into the same clusters as the wound samples from eight sites. [ABSTRACT FROM AUTHOR]

Carbon-fiber-reinforced plastics (CFRPs) are used as structural materials in the aircraft and automotive industries owing to their lightweight and high strength. With increasing global demand for CRFPs, their application as an alternative to metals is expected to expand to several other fields. Consequently, carbon fiber (CF) products, such as CFRPs, have been attracting attention, and are used worldwide. However, there is little scientific evidence on the safety of CFs. In addition, problems similar to those caused by microplastics will ultimately arise if milled CFs or CF dust are released into the aquatic environment. Therefore, on the basis of existing microplastics studies, we conducted a CF ecotoxicity experiment using Japanese medaka and confirmed that the medaka were harmed by fine CF particles in an aquatic environment under static conditions, such as stagnant water, although the CFs themselves did not exhibit notable toxicity. It is possible that the rate of infection by microorganisms increased as a result. [ABSTRACT FROM AUTHOR]

Sponges (phylum Porifera) harbour specific microbial communities that drive the ecology and evolution of the host. Understanding the structure and dynamics of these communities is emerging as a primary focus in marine microbial ecology research. Much of the work to date has focused on sponges from warm and shallow coastal waters, while sponges from the deep ocean remain less well studied. Here, we present a metataxonomic analysis of the microbial consortia associated with 23 individual deep-sea sponges. We identify a high abundance of archaea relative to bacteria across these communities, with certain sponge microbiomes comprising more than 90 % archaea. Specifically, the archaeal family Nitrosopumilaceae is prolific, comprising over 99 % of all archaeal reads. Our analysis revealed that sponge microbial communities reflect the host sponge phylogeny, indicating a key role for host taxonomy in defining microbiome composition. Our work confirms the contribution of both evolutionary and environmental processes to the composition of microbial communities in deep-sea sponges.

Odontogenic abscesses are usually caused by bacteria of the oral microbiome. However, the diagnostic culture of these bacteria is often prone to errors and sometimes fails completely due to the fastidiousness of the relevant bacterial species. The question arises whether additional pathogen diagnostics using molecular methods provide additional benefits for diagnostics and therapy. Experimental 16S rRNA gene analysis with next-generation sequencing (NGS) and bioinformatics was used to identify the microbiome of the pus in patients with severe odontogenic infections and was compared to the result of standard diagnostic culture. The pus microbiome was determined in 48 hospitalized patients with a severe odontogenic abscess in addition to standard cultural pathogen detection. Cultural detection was possible in 41 (85.42%) of 48 patients, while a pus-microbiome could be determined in all cases. The microbiomes showed polymicrobial infections in 46 (95.83%) cases, while the picture of a mono-infection occurred only twice (4.17%). In most cases, a predominantly anaerobic spectrum with an abundance of bacteria was found in the pus-microbiome, while culture detected mainly Streptococcus, Staphylococcus, and Prevotella spp. The determination of the microbiome of odontogenic abscesses clearly shows a higher number of bacteria and a significantly higher proportion of anaerobes than classical cultural methods. The 16S rRNA gene analysis detects considerably more bacteria than conventional cultural methods, even in culture-negative samples. Molecular methods should be implemented as standards in medical microbiology diagnostics, particularly for the detection of polymicrobial infections with a predominance of anaerobic bacteria.

Severe odontogenic abscesses are regularly caused by bacteria of the physiological oral microbiome. However, the culture of these bacteria is often prone to errors and sometimes does not result in any bacterial growth. Furthermore, various authors found completely different bacterial spectra in odontogenic abscesses. Experimental 16S rRNA gene next-generation sequencing analysis was used to identify the microbiome of the saliva and the pus in patients with a severe odontogenic infection. The microbiome of the saliva and the pus was determined for 50 patients with a severe odontogenic abscess. Perimandibular and submandibular abscesses were the most commonly observed diseases at 15 (30%) patients each. Polymicrobial infections were observed in 48 (96%) cases, while the picture of a mono-infection only occurred twice (4%). On average, 31.44 (±12.09) bacterial genera were detected in the pus and 41.32 (±9.00) in the saliva. In most cases, a predominantly anaerobic bacterial spectrum was found in the pus, while saliva showed a similar oral microbiome to healthy individuals. In the majority of cases, odontogenic infections are polymicrobial. Our results indicate that these are mainly caused by anaerobic bacterial strains and that aerobic and facultative anaerobe bacteria seem to play a more minor role than previously described by other authors. The 16S rRNA gene analysis detects significantly more bacteria than conventional methods and molecular methods should therefore become a part of routine diagnostics in medical microbiology.

Urine microbial fuel cells (MFCs) show potential for urine treatment to achieve simultaneous organic matter removal and electricity production. However, factors affecting the performance of urine MFCs during scaling up remain unclear. This study develops a 3D-printed air-cathode urine MFC with the membrane electrode assembly (MEA). After scale-up in parallel, unstable anode potential is responsible for the open circuit voltage (OCV) difference among various units, which leads to the energy loss in the system. For systems connected in series, unstable cathode potential mainly contributes to the voltage reversal, resulting in large power loss. Electrochemical impedance spectroscopy analysis indicates dramatically increased ohmic and polarization resistance in both serial and parallel systems. Bode plot further demonstrates after parallel connection, an obvious capacitance effect is observed, which provides evidence to illustrate the phenomenon of non-Faradaic current. Compared to serially connected systems, the capacitor of power management system can harvest more energy from systems connected in parallel. The microbial community analysis demonstrates Geobacter is the most dominant anodic electroactive bacteria both before and after scale-up. Overall, these results show the different strategic improvement should be executed while utilizing parallel connection (focusing on anode) or serial connection (focusing on cathode) to scale up urine MFCs. [Display omitted] • 3D-printed urine MFCs were fabricated with AEM-based MEA as the cathode. • Optimized MEA contained the AEM, cathodic electrode, diffusion and catalyst layer. • Voltage reversal and non-Faradaic current on the scale-up performance are evaluated. • Serial and parallel scale-up did not change the dominant electroactive bacteria. • Bray-Curtis similarity indicated microbial community shifted closer after scaling up. [ABSTRACT FROM AUTHOR]

The human gastric lumen is one of the most hostile environments of the human body suspected to be sterile until the discovery of Helicobacter pylori (H.p.). State of the art next generation sequencing technologies multiply the knowledge on H.p. functional genomics as well as on the colonization of supposed sterile human environments like the gastric habitat. Here we studied in a prospective, multicenter, clinical trial the 16S rRNA gene amplicon based bacterial microbiome in a total of 30 homogenized and frozen gastric biopsy samples from eight geographic locations. The evaluation of the samples for H.p. infection status was done by histopathology and a specific PCR assay. CagA status was determined by a CagA-specific PCR assay. Patients were grouped accordingly as H.p.-negative, H.p.-positive but CagA-negative and H.p.-positive and CagA-positive (n = 10, respectively). Here we show that H.p. infection of the gastric habitat dominates the gastric microbiota in most patients and is associated with a significant decrease of the microbial alpha diversity from H.p. negative to H.p. positive with CagA as a considerable factor. The genera Actinomyces, Granulicatella, Veillonella, Fusobacterium, Neisseria, Helicobacter, Streptococcus, and Prevotella are significantly different between the H.p.-positive and H.p.-negative sample groups. Differences in microbiota found between CagA-positive and CagA-negative patients were not statistically significant and need to be re-evaluated in larger sample cohorts. In conclusion, H.p. infection dominates the gastric microbiome in a multicentre cohort of patients with varying diagnoses.

Twenty-three bacterial strains were isolated from the secreted mucus trapping net of the marine polychaete Chaetopterus variopedatus (phylum Annelida) and twenty strains were identified using 16S rRNA gene analysis. Strain CB1-14 was recognized as a new species of the genus Vibrio using the eight-gene multilocus sequence analysis (MLSA) and genome sequences of nineteen type Vibrio strains. This Vibrio sp. was cultured, and 6-epi-monanchorin (2), previously isolated from the polychaete and two sponge species, was found in the cells and culture broth. The presence of the 6-epi-monanchorin was confirmed by its isolation followed by 1H NMR and HRESIMS analysis. These results showed the microbial origin of the bicyclic guanidine alkaloid 2 in C. variopedatus.

The human gastric lumen is one of the most hostile environments of the human body suspected to be sterile until the discovery of Helicobacter pylori (H.p.). State of the art next generation sequencing technologies multiply the knowledge on H.p. functional genomics as well as on the colonization of supposed sterile human environments like the gastric habitat. Here we studied in a prospective, multicenter, clinical trial the 16S rRNA gene amplicon based bacterialmicrobiome in a total of 30 homogenized and frozen gastric biopsy samples fromeight geographic locations. The evaluation of the samples for H.p. infection status was done by histopathology and a specific PCR assay. CagA status was determined by a CagA-specific PCR assay. Patients were grouped accordingly as H.p.-negative, H.p.-positive but CagA-negative and H.p.-positive and CagA-positive (n = 10, respectively). Here we show that H.p. infection of the gastric habitat dominates the gastric microbiota in most patients and is associated with a significant decrease of the microbial alpha diversity from H.p. negative to H.p. positive with CagA as a considerable factor. The genera Actinomyces, Granulicatella, Veillonella, Fusobacterium, Neisseria, Helicobacter, Streptococcus, and Prevotella are significantly different between the H.p.- positive and H.p.-negative sample groups. Differences in microbiota found between CagA-positive and CagA-negative patients were not statistically significant and need to be re-evaluated in larger sample cohorts. In conclusion, H.p. infection dominates the gastric microbiome in a multicentre cohort of patients with varying diagnoses. [ABSTRACT FROM AUTHOR]

Copyright of Arquivo Brasileiro de Medicina Veterinária e Zootecnia is the property of Universidade Federal de Minas Gerais, Escola de Veterinaria and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Coral reefs are keystone ecosystems, and the ecological success of coral reefs depends on coral-algal symbiosis and healthy coral-bacterial interactions. However, the bacteriome diversity associated with different coral species in the Gulf of Kutch, Gujarat, remains largely unexplored. In this study, we compared the bacteriome diversity of reef-building corals Goniopora (G. columna, G. lobata, G. stutchburyi) and Favia (F. favus) collected from the two islands viz. Poshitra (PO) and Pirotan (PI) in the Gulf of Kutch, Gujarat, using metagenomic sequencing of 16S rRNA gene and amplicon sequence variants (ASVs) based multivariate analysis. Heat map and network analyses were performed to explore coral bacteriome co-occurrence patterns, revealing 77 and 33 co-occurring bacterial genera associated with Goniopora sp. and F. favus corals, respectively. Co-occurring bacterial genera play a potential role in biogeochemical cycles like carbon, nitrogen, sulfur, nutrient metabolism, host detoxification, and association with dinoflagellates of the family Symbiodiniaceae. The majority of the bacterial genera present were frequently found in the corals, where some are predicted to play a significant role in coral resilience and have medicinal and biotechnological applications. These results indicate that the coral type, species difference, and location, in conjunction with environmental niche, play key roles in coral-bacteriome interaction. The present study can also serve as a baseline and pave the way for the conservation and transplantation of coral species in the Gulf of Kutch. [Display omitted] • Coral bacteriome diversity and comparative analyses of Goniopora sp. and Favia favus from two islands in the Gulf of Kutch. • Core bacteriome analysis and co-occurrence network analysis revealed the dominant and co-occurring taxa among the corals. • Our study revealed the potential roles of co-occuring bacterial genera in the coral ecosystem. • Coral type, species difference, geographic location, and surrounding niche play key roles in coral-bacteriome interaction. • This study, for the first time, reveals the baseline coral bacteriome diversity in the Gulf of Kutch, Gujarat. [ABSTRACT FROM AUTHOR]

A novel bacterial species is described that was isolated from the soil of Norrbyskär island (Sweden). This Gram-negative, facultatively anaerobic and motile rod, designated 17-6 T , was classified in the family Chromobacteriaceae , class Betaproteobacteria , and further characterized by a polyphasic approach. Comparative 16S rRNA gene analysis revealed the potential species novelty of the strain, with Silvimonas terrae (98.20 % similarity) and Silvimonas amylolytica (98.13 %) being its closest type strains. The phylogenetic novelty of the isolate at the level of species was confirmed using phylogenetic analyses based on the whole genome: average nucleotide identity values ranged from 79 to 81 %, average amino acid identity values from 75 to 81 % and percentage of conserved proteins values from 69-81 % with the members of genera Silvimonas and Amantichitinum . On the basis of phenotypic, phylogenetic, functional and genotypic analyses, we propose the isolate as the type strain of a novel species within the genus Silvimonas with the designation Silvimonas soli 17-6 T (=DSM 115342 T =CCM 9308 T ).

Background: Increasing age, several co-morbidities, environmental contamination, antibiotic exposure and other intestinal perturbations appear to be the greatest risk factors for C. difficile infection (CDI). Therefore, elderly care home residents are considered particularly vulnerable to the infection. The main objective of this study was to evaluate and follow the prevalence of C. difficile in 23 elderly care home residents weekly during a 4-month period. A C. difficile microbiological detection scheme was performed along with an overall microbial biodiversity study of the faeces content by 16S rRNA gene analysis. Results: Seven out of 23 (30.4 %) residents were (at least one week) positive for C. difficile. C. difficile was detected in 14 out of 30 diarrhoeal samples (43.7 %). The most common PCR-ribotype identified was 027. MLVA showed that there was a clonal dissemination of C. difficile strains within the nursing home residents. 16S-profiling analyses revealed that each resident has his own bacterial imprint, which was stable during the entire study. Significant changes were observed in C. difficile positive individuals in the relative abundance of a few bacterial populations, including Lachnospiraceae and Verrucomicrobiaceae. A decrease of Akkermansia in positive subjects to the bacterium was repeatedly found. Conclusions: A high C. difficile colonisation in nursing home residents was found, with a predominance of the hypervirulent PCR-ribotype 027. Positive C. difficile status is not associated with microbiota richness or biodiversity reduction in this study. The link between Akkermansia, gut inflammation and C. difficile colonisation merits further investigations. [ABSTRACT FROM AUTHOR]

The complex and enormous diversity of microorganisms associated with plant roots is important for plant health and growth and is shaped by numerous factors. This study aimed to unravel the effects of the soil type on bacterial communities in the rhizosphere of field-grown lettuce. We used an experimental plot system with three different soil types that were stored at the same site for ten years under the same agricultural management to reveal differences directly linked to the soil type and not influenced by other factors such as climate or cropping history. Bulk soil and rhizosphere samples were collected three and seven weeks after planting. The analysis of 16S rRNA gene fragments amplified from total community DNA by denaturing gradient gel electrophoresis and pyrosequencing revealed soil type-dependent differences in the bacterial community structure of the bulk soils and the corresponding rhizospheres. The rhizosphere effect differed depending on the soil type and the plant growth developmental stage. Despite the soil type-dependent differences in the bacterial community composition several genera such as Sphingomonas, Rhizobium, Pseudomonas and Variovorax were significantly increased in the rhizosphere of lettuce grown in all three different soils. The number of rhizosphere responders was highest three weeks after planting. Interestingly, in the soil with the highest numbers of responders the highest shoot dry weights were observed. Heatmap analysis revealed that many dominant operational taxonomic units were shared among rhizosphere samples of lettuce grown in diluvial sand, alluvial loam, and loess loam and that only a subset was increased in relative abundance in the rhizosphere compared to the corresponding bulk soil. The findings of the study provide insights into the effect of soil types on the rhizosphere microbiome of lettuce.

Efficient biofilm forming PGPR is expected to perform better under field conditions due to enhanced root colonization and survival under stress condition. Therefore, in this study 14 isolates of Bacillus sp. were selected after random screening based on multiple plant growth promoting traits like phosphate solubilization, production of indole acetic acid, siderophore, HCN, ammonia, EPS and ACC deaminase activity. Biofilm formation was studied in vitro by using 96 well polystyrene plate. Based on in vitro biofilm formation these isolates were grouped as moderate and strong biofilm former. Two isolates of Bacillus subtilis (BD6 and BCH4) identified by 16S rRNA gene sequence analysis exhibited multiple PGP traits but differed in their biofilm forming capacity were evaluated for root colonization and biofilm formation on the root surface. Biofilm was characterized by scanning electron and confocal laser scanning microscopy. Colonization studies revealed that isolate BCH4 colonized wheat roots more strongly compared to BD6 and form a biofilm on the root surface. Inoculation response to wheat showed an increase in plant vegetative growth parameters compared to control in a pot culture assay indicating that BCH4 a strong biofilm former with multiple PGP traits may be considered for further development as bioinoculant. [ABSTRACT FROM AUTHOR]

Background: Recently, there has been tremendous interest in the sinus microbiome and how it relates to disease. However, a lack of a standardized sample collection and DNA extraction methods makes comparison of results across studies nearly impossible. Furthermore, current techniques fail to identify which components of the microbiome are actually alive within the host at the time of sampling. Objective: To develop and optimize a method to differentiate which bacterial species in the human sinus microbiome are live versus dead. Methods: Duplicate samples from the middle meatus of patients with healthy sinus tissue and those patients with chronic rhinosinusitis were collected by using brushes (n = 12), swabs (n = 27), and tissue biopsy (n = 8) methods. One sample from each pair was either deoxyribonuclease I- or control-treated before DNA extraction. The relative bacterial versus human composition of each sample was determined. A 16S ribosomal RNA gene analysis was performed on a six-paired sample from patients with healthy sinus tissue. Results: We found that swabs and brushes collected a higher percentage of bacterial DNA than did tissue biopsy. We also determined that as much as 50% of the bacteria collected in these samples was already dead at the time of collection. The 16S ribosomal RNA gene analysis found significant changes in the relative abundance of taxa identified in the live versus dead bacterial communities of healthy human sinuses. Conclusions: Our findings indicated that swabs provided the best quality microbiome samples and that a large portion of the bacteria identified in the sinus were deoxyribonuclease I sensitive. These results highlighted the need for improved techniques such as those presented here, which can differentiate between living and dead bacteria in a sample, a potentially critical distinction when examining changes in sinus innate immune function because both components play important, but distinct, functions. Further studies will determine how these living and dead bacterial populations shift in different disease states and after clinical intervention. [ABSTRACT FROM AUTHOR]

In present study, several marine water samples collected from the North Goa Beaches, India for isolation of luminescent bacterial species. Isolates obtained labelled as DP1-5 and AB1-6. Molecular characterization including identification of a microbial culture using 16S rRNA gene based molecular technique and phylogenetic analysis confirmed that DP3 & AB1 isolates were Vibrio harveyi. All of the isolates demonstrated multiple metal resistances in terms of growth, with altered luminescence with variable metal concentration. Present investigations were an attempt towards exploring and reporting an updated diversity of bioluminescent bacterial species from various sites around the Goa, India which would be explored in future for constructing luminescence based biosensor for efficiently monitoring the level of hazardous metals in the environment. [ABSTRACT FROM AUTHOR]

Background. We sought to describe the temporal relationship between vaginal microbiota and human papillomavirus (HPV) detection.Methods. Thirty-two reproductive-age women self-collected midvaginal swabs twice weekly for 16 weeks (937 samples). Vaginal bacterial communities were characterized by pyrosequencing of barcoded 16S rRNA genes and clustered into 6 community state types (CSTs). Each swab was tested for 37 HPV types. The effects of CSTs on the rate of transition between HPV-negative and HPV-positive states were assessed using continuous-time Markov models.Results. Participants had an average of 29 samples, with HPV point prevalence between 58%–77%. CST was associated with changes in HPV status (P < .001). Lactobacillus gasseri–dominated CSTs had the fastest HPV remission rate, and a low Lactobacillus community with high proportions of the genera Atopobium (CST IV-B) had the slowest rate compared to L. crispatus–dominated CSTs (adjusted transition rate ratio [aTRR], 4.43, 95% confidence interval [CI], 1.11–17.7; aTRR, 0.33, 95% CI, .12–1.19, respectively). The rate ratio of incident HPV for low Lactobacillus CST IV-A was 1.86 (95% CI, .52–6.74).Conclusions. Vaginal microbiota dominated by L. gasseri was associated with increased clearance of detectable HPV. Frequent longitudinal sampling is necessary for evaluation of the association between HPV detection and dynamic microbiota. [ABSTRACT FROM AUTHOR]

Background: Smoking has been identified in observational studies as a risk factor for bacterial vaginosis (BV), a condition defined in part by decimation of Lactobacillus spp. The anti-estrogenic effect of smoking and trace amounts of benzo[a]pyrene diol epoxide (BPDE) may predispose women to BV. BPDE increases bacteriophage induction in Lactobacillus spp. and is found in the vaginal secretions of smokers. We compared the vaginal microbiota between smokers and non-smokers and followed microbiota changes in a smoking cessation pilot study. Methods: In 2010–2011, 20 smokers and 20 non-smokers were recruited to a cross-sectional study (Phase A) and 9 smokers were enrolled and followed for a 12-week smoking cessation program (Phase B). Phase B included weekly behavioral counseling and nicotine patches to encourage smoking cessation. In both phases, participants self-collected mid-vaginal swabs (daily, Phase B) and completed behavioral surveys. Vaginal bacterial composition was characterized by pyrosequencing of barcoded 16S rRNA genes (V1-V3 regions). Vaginal smears were assigned Nugent Gram stain scores. Smoking status was evaluated (weekly, Phase B) using the semi-quantitative NicAlert® saliva cotinine test and carbon monoxide (CO) exhalation. Results: In phase A, there was a significant trend for increasing saliva cotinine and CO exhalation with elevated Nugent scores (P value <0.005). Vaginal microbiota clustered into three community state types (CSTs); two dominated by Lactobacillus (L. iners, L. crispatus), and one lacking significant numbers of Lactobacillus spp. and characterized by anaerobes (termed CST-IV). Women who were observed in the low-Lactobacillus CST-IV state were 25-fold more likely to be smokers than those dominated by L. crispatus (aOR: 25.61, 95 % CI: 1.03-636.61). Four women completed Phase B. One of three who entered smoking cessation with high Nugent scores demonstrated a switch from CST-IV to a L.iners-dominated profile with a concomitant drop in Nugent scores which coincided with completion of nicotine patches. The other two women fluctuated between CST-IV and L. iners-dominated CSTs. The fourth woman had low Nugent scores with L. crispatus-dominated CSTs throughout. Conclusion: Smokers had a lower proportion of vaginal Lactobacillus spp. compared to non-smokers. Smoking cessation should be investigated as an adjunct to reducing recurrent BV. Larger studies are needed to confirm these findings. [ABSTRACT FROM AUTHOR]

Background: The sequences of the 16S rRNA genes extracted from fecal samples provide insights into the dynamics of fecal microflora. This potentially gives valuable etiological information for patients whose conditions have been ascribed to unknown pathogens, which cannot be accomplished using routine culture methods. We studied 33 children with diarrhea who were admitted to the Children's Hospital in Shanxi Province during 2006. Results: Nineteen of 33 children with diarrhea could not be etiologically diagnosed by routine culture and polymerase chain reaction methods. Eleven of 19 children with diarrhea of unknown etiology had Streptococcus as the most dominant fecal bacterial genus at admission. Eight of nine children whom three consecutive fecal samples were collected had Streptococcus as the dominant fecal bacterial genus, including three in the Streptococcus bovis group and three Streptococcus sp., which was reduced during and after recovery. We isolated strains that were possibly from the S. bovis group from feces sampled at admission, which were then identified as Streptococcus lutetiensis from one child and Streptococcus gallolyticus subsp. pasteurianus from two children. We sequenced the genome of S. lutetiensis and identified five antibiotic islands, two pathogenicity islands, and five unique genomic islands. The identified virulence genes included hemolytic toxin cylZ of Streptococcus agalactiae and sortase associated with colonization of pathogenic streptococci. Conclusions: We identified S. lutetiensis and S. gallolyticus subsp. pasteurianus from children with diarrhea of unknown etiology, and found pathogenic islands and virulence genes in the genome of S. lutetiensis. [ABSTRACT FROM AUTHOR]

Abstract: The addition of commercial nitrifying bacterial products has resulted in significant improvement of nitrification efficiency in recirculating aquaculture systems (RAS). We developed two nitrifying bacterial consortia (NBC) from marine and brackish water as start up cultures for immobilizing commercialized nitrifying bioreactors for RAS. In the present study, the community compositions of the NBC were analyzed by universal 16S rRNA gene and bacterial amoA gene sequencing and fluorescence in situ hybridization (FISH). This study demonstrated that both the consortia involved autotrophic nitrifiers, denitrifiers as well as heterotrophs. Abundant taxa of the brackish water heterotrophic bacterial isolates were Paenibacillus and Beijerinckia spp. whereas in the marine consortia they were Flavobacterium, Cytophaga and Gramella species. The bacterial amoA clones were clustered together with high similarity to Nitrosomonas sp. and uncultured beta Proteobacteria. FISH analysis detected ammonia oxidizers belonging to β subclass of proteobacteria and Nitrosospira sp. in both the consortia, and Nitrosococcus mobilis lineage only in the brackish water consortium and the halophilic Nitrosomonas sp. only in the marine consortium. However, nitrite oxidizers, Nitrobacter sp. and phylum Nitrospira were detected in both the consortia. The metabolites from nitrifiers might have been used by heterotrophs as carbon and energy sources making the consortia a stable biofilm. [Copyright &y& Elsevier]

Abstract: Ten metalworking fluids (MWF) and seven water preparation basis samples (WPB) were taken from five industrial plants in Germany. Total cells (TCC) and colony forming units (CFU) were counted, strains were isolated and their 16S rRNA gene was sequenced. Additionally, DNA was extracted directly from the samples, and clone libraries of 16S rRNA genes were built and gene sequenced. TCC ranged from 7.6×104 TCC/mL MWF to 1.6×108 TCC/mL MWF, and from 4.6×102 TCC/mL WPB to 7.8×107 TCC/mL WPB. The CFU showed similar but often lower results. A total of 70 isolates and 732 clones were 16S rRNA gene sequenced and all isolates, as well as 183 of the nearly full length 16S rRNA of these clones, were gene sequenced. A total of 98 different genera were detected in all 17 samples. The number of genera within each sample varied highly, with 1–22 genera per sample. The dominant genera in MWF were Leucobacter, Desemzia, Sphingomonas and Wautersiella. From these, only Sphingomonas was detected in WPB as well. This study showed that MWF can harbour a high bacterial diversity, which differs significantly from the bacterial flora of the corresponding WPB. [Copyright &y& Elsevier]

A Gram-negative, facultatively anaerobic, motile by means of single polar flagellum, rod-shaped marine bacterium, designated strain E414, was isolated from sea water collected from a farming pond rearing marine shrimp Litopenaeus vannamei in Zhanjiang, Guangdong province, PRC. The strain was able to grow in the presence of 0.5-6% (w/v) NaCl (optimally in 3-6% (w/v) NaCl), between pH 6 and 9 (optimally at pH 7-8), between 15 and 37°C (optimally at 25-30°C). Phylogenetic analysis based on 16S rRNA gene sequences locate strain E414 in the vicinity of the coralliilyticus clade within the genus Vibrio. DNA-DNA relatedness data and multigene phylogenetic analysis based on the concatenated sequences of four genes (16S rRNA, rpoA, recA and pyrH) clearly differentiated strain E414 from its closest phylogenetic neighbours. Analysis of phenotypic features, including enzyme activities and utilization and fermentation of various carbon sources, further revealed discrimination between strain E414 and phylogenetically related Vibrio species. The major fatty acid components are Cω6c and/or Cω7c (27.4%), Cω7c and/or Cω6c (19.3%) and C (18.2%). The DNA G+C content of strain E414 was 38.7 mol%. Based on phenotypic, chemotaxonomic, phylogenetic and DNA-DNA relatedness values, it can be concluded that E414 should be placed in the genus Vibrio as representing a novel species, for which the name Vibrio zhanjiangensis sp. nov. is proposed, with the type strain E414 (=CCTCC AB 2011110 = NBRC 108723 = DSM 24901). [ABSTRACT FROM AUTHOR]

Phylogenetic diversities of the endolithic bacterial communities in dolomite and limestone rocks from a karst canyon (Nanjiang Canyon), China, were analyzed based on the 16S rRNA gene analysis. In the dolomite endolithic bacterial communities, members of Cyanobacteria were the most abundant followed in abundance by members of Alphaproteobacteria, Acidobacteria, and Actinobacteria. Members of Betaproteobacteria, Deltaproteobacteria, Bacteriodetes, Verrucomicrobia, and Chloroflexi were also present. Large percentages of bacterial clones in the limestone were related to the Actinobacteria, Alphaproteobacteria, and Cyanobacteria. In addition, members of Deltaproteobacteria, Bacteriodetes, Chloroflexi, Acidobacteria, Firmicutes, Planctomycetes, and Candidate division TM7 were identified. Slight differences in endolithic bacterial abundance and community structure existed between the dolomite and limestone rocks. These rock microorganisms are inferred to have played an important role in the formation of Karst soil from carbonate rocks during a long geological history. [ABSTRACT FROM AUTHOR]

Abstract: A polyphasic taxonomic study was performed on seven Bacillus-like bacteria isolated from three hypersaline and alkaline lakes located in China, Kenya and Tanzania. All strains were moderately halophilic and alkaliphilic, Gram positive, motile rods. The DNA G+C content from the seven isolates ranged from 42.2 to 43.4mol% and their major fatty acid was anteiso-C15:0. Strain CG1T, selected as representative strain of the isolates, possesses meso-diaminopimelic acid in the cell wall peptidoglycan, MK-7 as the predominant menaquinone and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as the major polar lipids. Comparative 16S rRNA gene sequence analysis indicated that the isolates belonged to the genus Bacillus. The seven isolates shared 97.7–99.9% 16S rRNA gene sequence similarity, and formed a branch that was distinct from the type strains of the recognized species of the genus Bacillus. They were most closely related to Bacillus agaradhaerens DSM 8721T (92.6–93.8% 16S rRNA sequence similarity). DNA–DNA hybridization values between the seven isolates were 85–100%. According to the polyphasic characterization, the strains represent a novel species, for which the name Bacillus locisalis sp. nov. is proposed. The type strain is CG1T (CCM 7370T =CECT 7152T =CGMCC 1.6286T =DSM 18085T). [Copyright &y& Elsevier]