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A Gram-stain-negative, obligately anaerobic, non-motile, non-spore-forming, long-rod-shaped and non-flagellated bacterial strain, designated T3-2 S1-C T , was isolated from a sediment sample collected at the Okinawa Trough. Phylogenetic analyses of 16S rRNA gene sequences and the whole genome revealed that strain T3-2 S1-C T was a member of the family Marinifilaceae and exhibited less than 95.1 % sequence similarities to the closely related type strains of the family Marinifilaceae . Optimal growth occurred at pH 7.0, 28 °C and in the presence of 3 % (w/v) NaCl. The isoprenoid quinone of strain T3-2 S1-C T was identified as menaquinone-7 (MK-7) and the predominant fatty acids (>10 %) were iso-C 15 : 0 (38.9 %) and anteiso-C 15 : 0 (11.6 %). The major polar lipids were one phosphatidylethanolamine, one phosphatidylmonomethylethanolamine, one aminolipids, two unidentified lipids and two unidentified phospholipids. The DNA G+C content of strain T3-2 S1-C T was 35.7 mol%. On the basis of the results of polyphasic analyses, strain T3-2 S1-C T is considered to represent a novel species of the genus Ancylomarina , for which the name Ancylomarina longa sp. nov. is proposed. The type strain is T3-2 S1-C T (=KCTC 15505 T =MCCC 1K01617 T ).

Arsenic is a toxin, ranking first on the Agency for Toxic Substances and Disease Registry and the Environmental Protection Agency Priority List of Hazardous Substances. Chronic exposure increases the risk of a broad range of human illnesses, most notably cancer; however, there is significant variability in arsenic-induced disease among exposed individuals. Human genetics is a known component, but it alone cannot account for the large inter-individual variability in the presentation of arsenicosis symptoms. Each part of the gastrointestinal tract (GIT) may be considered as a unique environment with characteristic pH, oxygen concentration, and microbiome. Given the well-established arsenic redox transformation activities of microorganisms, it is reasonable to imagine how the GIT microbiome composition variability among individuals could play a significant role in determining the fate, mobility and toxicity of arsenic, whether inhaled or ingested. This is a relatively new field of research that would benefit from early dialogue aimed at summarizing what is known and identifying reasonable research targets and concepts. Herein, we strive to initiate this dialogue by reviewing known aspects of microbe-arsenic interactions and placing it in the context of potential for influencing host exposure and health risks. We finish by considering future experimental approaches that might be of value., (© 2019 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Objectives: Many countries use faecal immunochemical testing (FIT) to screen for colorectal cancer. There is increasing evidence that faecal microbiota play a crucial role in colorectal cancer carcinogenesis. We assessed the possibility of measuring faecal microbial features in FIT as potential future biomarkers in colorectal cancer screening., Methods: Bacterial stability over time and the possibility of bacterial contamination were evaluated using quantitative polymerase chain reaction analysis. Positive FIT samples ( n  = 200) of an average-risk screening cohort were subsequently analysed for universal 16S, and bacteria . Escherichia coli ( E. coli ), Fusobacterium nucleatum ( F. nucleatum ), Bacteroidetes and Faecalibacterium prausnitzii ( F. prausnitzii ) by qPCR. The results were compared with colonoscopy findings., Results: Faecal microbiota in FIT were stably measured up to six days for E. coli ( p  = 0.53), F. nucleatum ( p  = 0.30), Bacteroidetes (p = 0.05) and F. prausnitzii ( p  = 0.62). Overall presence of bacterial contamination in FIT controls was low. Total bacterial load (i.e. 16S) was significantly higher in patients with colorectal cancer and high-grade dysplasia ( p  = 0.006). For the individual bacteria tested, no association was found with colonic lesions., Conclusions: These results show that the faecal microbial content can be measured in FIT samples and remains stable for six days. Total bacterial load was higher in colorectal cancer and high-grade dysplasia. These results pave the way for further research to determine the potential role of microbiota assessment in FIT screening.

Altered intestinal microbiota is associated with systemic and intestinal diseases, such as inflammatory bowel disease (IBD). Dysbiotic microbiota with enhanced proinflammatory capacity is characterized by depletion of anaerobic commensals, increased proportion of facultatively anaerobic bacteria, as well as reduced diversity and stability. In this study, we developed a high-throughput in vitro screening assay to isolate intestinal commensal bacteria with anti-inflammatory capacity from a healthy fecal microbiota transplantation donor. Freshly isolated gut bacteria were screened for their capacity to attenuate Escherichia coli lipopolysaccharide (LPS)-induced interleukin 8 (IL-8) release from HT-29 cells. The screen yielded a number of Bacteroides and Parabacteroides isolates, which were identified as P. distasonis , B. caccae , B. intestinalis , B. uniformis , B. fragilis , B. vulgatus and B. ovatus using whole genome sequencing. We observed that a cell-cell contact with the epithelium was not necessary to alleviate in vitro inflammation as spent culture media from the isolates were also effective and the anti-inflammatory action did not correlate with the enterocyte adherence capacity of the isolates. The anti-inflammatory isolates also exerted enterocyte monolayer reinforcing action and lacked essential genes to synthetize hexa-acylated, proinflammatory lipid A, part of LPS. Yet, the anti-inflammatory effector molecules remain to be identified. The Bacteroides strains isolated and characterized in this study have potential to be used as so-called next-generation probiotics., Competing Interests: The authors declare no conflict of interest.

Recent studies have used ethanol stool disinfection as a mean of promoting valuable species' cultivation in bacteriotherapy trials for Clostridium difficile infections (CDI) treatment with a particular focus on sporulating bacteria. Moreover, the culturomic approach has considerably enriched the repertoire of cultivable organisms in the human gut in recent years. This study aimed to apply this culturomic approach on fecal donor samples treated with ethanol disinfection to evidence potential beneficial microbes that could be used in bacteriotherapy trials for the treatment of CDI. Thereby, a total of 254 bacterial species were identified, 9 of which were novel. Of these, 242 have never been included in clinical trials for the treatment of CDIs, representing potential new candidates for bacteriotherapy trials. While non-sporulating species were nevertheless more affected by the ethanol pretreatment than sporulating species, the ethanol disinfection technique did not specifically select bacteria able to sporulate, as suggested by previous studies. Furthermore, some bacteria previously considered as potential candidates for bacteriotherapy have been lost after ethanol treatment. This study, while enriching the bacterial repertoire of the human intestine, would nevertheless require determining the exact contribution of each of species composing the bacterial consortia intended to be administered for CDI treatment.

This study evaluated the modulation of gut microbiota, immune responses, and gut morphometry in C57BL/6 mice, upon oral administration of S. maxima -derived modified pectin (SmP, 7.5 mg/mL) and pectin nanoparticles (SmPNPs; 7.5 mg/mL). Metagenomics analysis was conducted using fecal samples, and mice duodenum and jejunum were used for analyzing the immune response and gut morphometry, respectively. The results of metagenomics analysis revealed that the abundance of Bacteroidetes in the gut increased in response to both modified SmP and SmPNPs (75%) as compared with that in the control group (66%), while that of Firmicutes decreased in (20%) as compared with that in the control group (30%). The mRNA levels of mucin, antimicrobial peptide, and antiviral and gut permeability-related genes in the duodenum were significantly ( p < 0.05) upregulated (> 2-fold) upon modified SmP and SmPNPs feeding. Protein level of intestinal alkaline phosphatase was increased (1.9-fold) in the duodenum of modified SmPNPs feeding, evidenced by significantly increased goblet cell density (0.5 ± 0.03 cells/1000 µm 2 ) and villi height (352 ± 10 µm). Our results suggest that both modified SmP and SmPNPs have the potential to modulate gut microbial community, enhance the expression of immune related genes, and improve gut morphology., Competing Interests: The authors declare that they have no conflict of interest.

Blue holes are unique geomorphological units characterized by steep redox and biogeochemical gradients. Yongle Blue Hole is located on the largest atoll (Yongle Atoll) of the western Xisha Islands in the South China Sea. A Gram-stain-negative, facultatively anaerobic, non-motile, non-flagellated marine bacterium with creamy white colonies, designated JC036 T , was isolated from Yongle Blue Hole. Cells were short-rod-shaped and catalase-negative. 16S rRNA gene sequence analysis showed that sequence similarities were lower than 91.6 % against all validly named species in the family Prolixibacteraceae ; a reconstructed phylogenetic tree indicated that strain JC036 T formed a lineage with strains in the family Prolixibacteraceae . Growth occurred at 4-37 °C (optimum, 28 °C), at pH 5.0-9.0 (optimum, 7.0) and in the presence of 2-6 % (w/v) NaCl (optimum, 3 %). The prevalent isoprenoid quinone of strain JC036 T was menaquinone-7 (MK-7). Iso-C 15 : 0 and iso-C 17 : 0 3-OH were the predominant fatty acids. The major polar lipids included a phospholipid, phosphatidylethanolamine, an aminophospholipid and four unidentified lipids. The genomic DNA G+C content of strain JC036 T was 37.8 mol%. Based on physiological and biochemical characteristics and whole genome comparisons, we propose a new genus and species, Puteibacter caeruleilacunae gen. nov., sp. nov., within the family Prolixibacteraceae . The type strain of Puteibacter caeruleilacunae is JC036 T (=JCM 33128 T =MCCC 1K03579 T ). From this study, a deeper understanding of the community of the microorganism and their roles in biogeochemical cycles, especially anaerobic bacteria, is provided.

Strain TTM-71 T , isolated from a freshwater river in Taiwan, was characterized using a polyphasic taxonomic approach. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set (92 protein clusters) indicated that strain TTM-71 T is affiliated with species in the genus Filimonas . The 16S rRNA gene sequence similarity indicated that strain TTM-71 T is closely related to species within the genus Filimonas (94.7-95.5 % sequence similarity) and had a high sequence similarity with Filimonas endophytica SR 2-06 T (95.5 %). Strain TTM-71 T showed 70.3 % average nucleotide identity and 24.9 % digital DNA-DNA hybridization identity with Filimonas lacunae YT21 T . Cells were Gram-stain-negative, aerobic, motile by gliding, rod-shaped and formed beige-colored colonies. Optimal growth occurred at 20 °C, pH 8, and in the presence of 0.5 % NaCl. The major fatty acids of strain TTM-71 T were iso-C 15 : 0 , iso-C 15 : 1 G and summed feature 3 (comprising C 16 : 1   ω 7c and/or C 16 : 1   ω 6c ). The predominant hydroxy fatty acid was iso-C 17 : 0 3-OH. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, four uncharacterized aminophospholipids, one uncharacterized aminolipid, one uncharacterized phospholipid and one uncharacterized lipid. The predominant polyamine was homospermidine. The only isoprenoid quinone was MK-7. Genomic DNA G+C content was 45.6 mol%. On the basis of the polyphasic evidence presented, strain TTM-71 T is considered to represent a novel species of the genus Filimonas , for which the name Filimonas effusa sp. nov. is proposed. The type strain is TTM-71 T (=BCRC 81160 T =LMG 31017 T =KCTC 62871 T ).

We describe a new multidrug resistant Chitinophaga species that was isolated from patients with type 2 diabetes in Vietnam. Strain BD 01 T was cultivated in 2017 from a blood sample of a patient suffering from bacteremia. Strain VP 7442 was isolated in 2018 from a pleural fluid sample of a patient who had presented with lung abscess and pleural effusion. Both strains are aerobic, Gram-negative, non-motile and non-spore-forming. The 16S rRNA gene sequences of both strains are 100 % similar and share a highest 16S sequence identity with Chitinophaga polysaccharea MRP-15 T of 97.42 %. Their predominant fatty acid is iso-C 15 : 0 (73.8 % for strain BD 01 T and 79.8 % for strain VP 7442). The draft genome sizes of strains BD 01 T and VP 7442 are 6 308 408 and 6 308 579 bp, respectively. They are resistant to beta-lactams, aminoglycosides, fluoroquinolones, metronidazole, fosfomycin, vancomycin and macrolides, and exhibit 20 and 18 antimicrobial resistance-related genes, respectively. Using the multiphasic taxonogenomic approach, we propose that strains BD 01 T (=CSUR P9622=VTCC 70981) and VP 7442 (=CSUR P9623=VTCC 70982) represent a new species, for which we propose the name Chitinophaga vietnamensis sp. nov. Strain BD 01 T was chosen as type strain of C. vietnamensis sp. nov.

The two common species of house dust mites (HDMs), Dermatophagoides farinae and D. pteronyssinus, are major sources of allergens in human dwellings worldwide. Many allergens from HDMs have been described, but their extracts vary in immunogens. Mite strains may differ in their microbiomes, which affect mite allergen expression and contents of bacterial endotoxins. Some bacteria, such as the intracellular symbiont Cardinium, can affect both the sex ratio and biochemical pathways of mites, resulting in abundance variations of mite allergens/immunogens. Here, we investigated the bacterial microbiomes of D. farinae and D. pteronyssinus males and females using barcode 16S rDNA sequencing, qPCR, and genomic data analysis. We found a single species of Cardinium associated with D. farinae strains from the USA, China and Europe. Cardinium had high abundance relative to other bacterial taxa and represented 99% of all bacterial DNA reads from female mites from the USA. Cardinium was also abundant with respect to the number of host cells-we estimated 10.4-11.8 cells of Cardinium per single female mite cell. In a European D. farinae strain, Cardinium was more prevalent in females than in males (representing 92 and 67% of all bacterial taxa in females and males, respectively). In contrast, D. pteronyssinus lacked any Cardinium species, and the microbiomes of male and female mites were similar. We produced a Cardinium genome assembly (1.48 Mb; GenBank: PRJNA555788, GCA&#95;007559345.1) associated with D. farinae. The ascertained ubiquity and abundance of Cardinium strongly suggest that this intracellular bacterium plays an important biological role in D. farinae.

Strain XY-J91 T , a Gram-stain-negative, reddish orange, non-spore-forming and short-rod-shaped marine bacterium, was isolated from rhizosphere soil of the mangrove plant Kandelia candel (L.) Druce in Mai Po Nature Reserve, Hong Kong. The strain showed growth at 15-50 °C (optimum 40 °C), at pH 5.5-9.5 (optimum 7.0-8.0) and with 0-8 % (w/v) NaCl (optimum 1-2 %). The only respiratory quinone was MK-7 and the major fatty acids were iso-C 15 : 0 and iso-C 17 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, an unidentified aminolipid and an unidentified phospholipid. The G+C content of strain XY-J91 T was 40.4 mol%. Strain XY-J91 T exhibited highest 16S rRNA gene sequence similarities to the type strains of Algoriphagus marincola SW-2 T (96.66 %), Algoriphagus taiwanensis CC-PR-82 T (96.21%), Algoriphagus ornithinivorans JC2052 T (96.16%), Algoriphagus confluentis HJM-2 T (95.73%) and Algoriphagus zhangzhouensis 12C11 T (95.52 %). Based on the phylogenetic, phenotypic and chemotaxonomic evidence presented, strain XY-J91 T represents a novel species of the genus Algoriphagus , for which the name Algoriphagus kandeliae sp. nov. is proposed. The type strain is XY-J91 T (=MCCC 1K03612 T =KCTC 72216 T ).

Inflammatory bowel diseases (IBD) are associated with alterations in gut microbial abundances and lumenal metabolite concentrations, but the effects of specific metabolites on the gut microbiota in health and disease remain largely unknown. Here, we analysed the influences of metabolites that are differentially abundant in IBD on the growth and physiology of gut bacteria that are also differentially abundant in IBD. We found that N-acylethanolamines (NAEs), a class of endogenously produced signalling lipids elevated in the stool of IBD patients and a T-cell transfer model of colitis, stimulated growth of species over-represented in IBD and inhibited that of species depleted in IBD in vitro. Using metagenomic sequencing, we recapitulated the effects of NAEs in complex microbial communities ex vivo, with Proteobacteria blooming and Bacteroidetes declining in the presence of NAEs. Metatranscriptomic analysis of the same communities identified components of the respiratory chain as important for the metabolism of NAEs, and this was verified using a mutant deficient for respiratory complex I. In this study, we identified NAEs as a class of metabolites that are elevated in IBD and have the potential to shift gut microbiota towards an IBD-like composition.

A novel facultative anaerobic and facultative psychrophilic bacterium, designated SPP2 T , was isolated from an Antarctic marine sediment. Cells of the isolate were observed to be long rods (0.5 × 5-10 μm), Gram-stain negative and to have gliding motility. For growth, the optimum NaCl concentration was found to be 2-3% and the optimum temperature to be 18-22 °C. Strain SPP2 T cannot use sulfate and nitrate as electron acceptors in the presence of lactate. The G+C content of the genomic DNA was determined to be 36.0 mol%.. The major cellular fatty acids were identified as anteiso-C 15:0 and iso-C 15:0 . MK-7 was found to be the predominant respiratory quinone. Phylogenetic analysis based on the 16S rRNA gene revealed that the novel strain belongs to the family Marinifilaceae and to be closely related to Labilibaculum manganireducens 59.10-2M T with 16S rRNA gene sequence identity of 98%. The OrthoANI and dDDH values between the genome sequences of strain SPP2 T and its close relative were 84% and 27.3%, which are lower than the threshold values for species delineation. On the basis of phylogenetic and phenotypic characterisation, Labilibaculum antarcticum sp. nov. is proposed with the type strain SPP2 T (= NBRC 111151 T  = CECT 9460 T ).

The human gut microbiota is affected by genetic and environmental factors. It remains unclear how host genetic and environmental factors affect the composition and function of gut microbiota in populations living at high altitudes. We used a metagenome-wide analysis to investigate the gut microbiota composition in 15 native Tibetans and 12 Hans living on the Tibetan Plateau. The composition of gut microbiota differed significantly between these two groups ( P < 0.05). The Planctomycetes was the most abundant phyla both in native Tibetans and in Hans. Furthermore, the most relatively abundant phyla for native Tibetans were Bacteroidetes (15.66%), Firmicutes (11.10%), Proteobacteria (1.32%), Actinobacteria (1.10%), and Tenericutes (0.35%), while the most relatively abundant phyla for Hans were Bacteroidetes (16.28%), Firmicutes (8.41%), Proteobacteria (2.93%), Actinobacteria (0.49%), and Cyanobacteria (0.21%). The abundance of the majority of genera was significantly higher in Tibetans than in Hans ( P < 0.01). The number of microbial genes was 4.9 times higher in Tibetans than in Hans. The metabolic pathways and clusters of orthologous groups differed significantly between the two populations ( P < 0.05). The abundance of carbohydrate-active enzyme modules and antibiotic resistance genes was significantly lower in Tibetans compared to Hans ( P < 0.05). Our results suggest that different genetic factors (race) and environmental factors (diets and consumption of antibiotics) may play important roles in shaping the composition and function of gut microbiota in populations living at high altitudes., Competing Interests: All authors declare that they have no conflict of interest., (Copyright © 2020 Kang Li et al.)

Introduction: Fecal microbiota transplantation (FMT) is recommended as safe and effective treatment for recurrent Clostridioides difficile infections. Freezing the FMT preparation simplifies the process, allowing a single stool sample to be used for multiple receivers and over an extended period of time. We aimed to assess the effect of long-term frozen storage on bacterial taxonomic profiles of a stool suspension prepared for FMT. Methods: DNA was extracted from a stool suspension before freezing and sequentially during the 18-month storage period at -80°C. Two different protocols were used for DNA extraction. The first relied on a classical mechanical and chemical cell disruption to extract both intra- and extracellular DNA; the second included specific pre-treatments aimed at removing free DNA and DNA from human and damaged bacterial cells. Taxonomic profiling of bacterial communities was performed by sequencing of V3-V4 16S rRNA gene amplicons. Results: Microbiota profiles obtained by whole DNA extraction procedure remained relatively stable during frozen storage. When DNA extraction procedure included specific pre-treatments, microbiota similarity between fresh and frozen samples progressively decreased with longer frozen storage times; notably, the abundance of Bacteroidetes decreased in a storage duration-dependent manner. The abundance of Firmicutes, the main butyrate producers in the colon, were not much affected by frozen storage for up to 1 year. Conclusion: Our data show that metataxonomic analysis of frozen stool suspensions subjected to specific pre-treatments prior to DNA extractions might provide an interesting indication of bacterial resistance to stress conditions and thus of chances of survival in FMT recipients., (Copyright © 2020 Dorsaz, Charretier, Girard, Gaïa, Leo, Schrenzel, Harbarth, Huttner and Lazarevic.)

Gut dysbiosis has been associated with several disease outcomes including diabetes in human populations. Currently, there are no studies of the gut microbiome composition in relation to type 2 diabetes (T2D) in Africans. Here, we describe the profile of the gut microbiome in non-diabetic adults (controls) and investigate the association between gut microbiota and T2D in urban West Africans. Gut microbiota composition was determined in 291 Nigerians (98 cases, 193 controls) using fecal 16S V4 rRNA gene sequencing done on the Illumina MiSeq platform. Data analysis of operational taxonomic units (OTU) was conducted to describe microbiome composition and identify differences between T2D and controls. The most abundant phyla were Firmicutes, Actinobacteria , and Bacteroidetes . Clostridiaceae , and Peptostreptococcaceaea were significantly lower in cases than controls ( p < 0.001). Feature selection analysis identified a panel of 18 OTUs enriched in cases that included Desulfovibrio piger, Prevotella, Peptostreptococcus, and Eubacterium . A panel of 17 OTUs that was enriched in the controls included Collinsella, Ruminococcus lactaris, Anaerostipes , and Clostridium . OTUs with strain-level annotation showing the largest fold-change included Cellulosilyticum ruminicola (log 2 FC = -3.1; p = 4.2 × 10 -5 ), Clostridium paraputrificum (log 2 FC = -2.5; p = 0.005), and Clostridium butyricum (log 2 FC = -1.76; p = 0.01), all lower in cases. These findings are notable because supplementation with Clostridium butyricum and Desulfovibrio piger has been shown to improve hyperglycemia and reduce insulin resistance in murine models. This first investigation of gut microbiome and diabetes in urban Africans shows that T2D is associated with compositional changes in gut microbiota highlighting the possibility of developing strategies to improve glucose control by modifying bacterial composition in the gut., (Copyright © 2020 Doumatey, Adeyemo, Zhou, Lei, Adebamowo, Adebamowo and Rotimi.)

The variation in microbial composition over time was assessed in biofilms formed in situ on selected non-food and food contact surfaces of meat and fish industries, previously identified as Listeria monocytogenes-positive foci. First, all samples were analysed for the detection and quantification of L. monocytogenes using ISO 11290-1 and ISO 11290-2 norms, respectively. Although the pathogen was initially detected in all samples, direct quantification was not possible. Psychrotrophic bacteria counts were among resident microbiota in meat industry samples (Mean max  = 6.14 log CFU/cm 2 ) compared to those form fish industry (Mean max  = 5.85 log CFU/cm 2 ). Visual analysis of the biofilms using epifluorescence microscopy revealed a trend to form microcolonies in which damaged/dead cells would act as anchoring structures. 16S rRNA gene metagenetic analysis demonstrated that, although Proteobacteria (71.37%) initially dominated the bacterial communities at one meat industry location, there was a dramatic shift in composition as the biofilms matured, where Actinobacteria (79.72%) became the major phylum present in later samples. This change was largely due to an increase of Nocardiaceae, Micrococcaceae and Microbacteriaceae. Nevertheless, for the other sampling location, the relative abundance of the dominating phylum (Firmicutes) remained consistent over the entire sampling period (Mean = 63.02%). In fish industry samples, Proteobacteria also initially dominated early on (90.69%) but subsequent sampling showed a higher diversity in which Bacteroidetes and Proteobacteria were the most abundant phyla accounting for the 48.04 and 37.98%, respectively by the last sampling period. Regardless of the location, the community profiles of the endpoint samples were similar to those reported previously. This demonstrated that in a given industrial setting there is a trend to establish a determinate biofilm structure due to the environmental factors and the constant incoming microbiota. This information could be used to improve the existing sanitisation protocols or for the design of novel strategies., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Microbial dysbiosis has long been postulated to be associated with the pathogenesis of inflammatory bowel disease (IBD). Although evidence supporting the anti-colitic effects of melatonin have been accumulating, it is not clear how melatonin affects the microbiota. Herein, we investigated the effects of melatonin on the microbiome in colitis and identified involvement of Toll-like receptor (TLR) 4 signalling in the effects. Melatonin improved dextran sulfate sodium (DSS)-induced colitis and reverted microbial dysbiosis in wild-type (WT) mice but not in TLR4 knockout (KO) mice. Induction of goblet cells was observed with melatonin administration, which was accompanied by suppression of Il1b and Il17a and induction of melatonin receptor and Reg3β, an antimicrobial peptide (AMP) against Gram-negative bacteria. In vitro, melatonin treatment of HT-29 intestinal epithelial cells promotes mucin and wound healing and inhibits growth of Escherichia coli. Herein, we showed that melatonin significantly increases goblet cells, Reg3β, and the ratio of Firmicutes to Bacteriodetes by suppressing Gram-negative bacteria through TLR4 signalling. Our study suggests that sensing of bacteria through TLR4 and regulation of bacteria through altered goblet cells and AMPs is involved in the anti-colitic effects of melatonin. Melatonin may have use in therapeutics for IBD.

The neonatal period, during which the initial gut microbiota is acquired, is a critical phase. The healthy development of the infant's microbiome can be interrupted by external perturbations, like antibiotics, which are associated with profound effects on the gut microbiome and various disorders later in life. The aim of this study was to investigate the development of intestinal microbiota and the effect of antibiotic exposure during the first three months of life in term infants. Fecal samples were collected from healthy infants and infants who received antibiotics in the first week of life at one week, one month, and three months after birth. Microbial composition was analyzed using IS-pro and compared between antibiotics-treated and untreated infants. In total, 98 infants, divided into four groups based on feeding type and delivery mode, were analyzed. At one week of age, samples clustered into two distinct groups, which were termed "settler types", based on their Bacteroidetes abundance. Caesarean-born infants belonged to the low-Bacteroidetes settler type, but vaginally-born infants were divided between the two groups. The antibiotics effect was assessed within a subgroup of 45 infants, vaginally-born and exclusively breastfed, to minimize the effect of other confounders. Antibiotics administration resulted in lower Bacteroidetes diversity and/or a delay in Bacteroidetes colonization, which persisted for three months, and in a differential development of the microbiota. Antibiotics resulted in pronounced effects on the Bacteroidetes composition and dynamics. Finally, we hypothesize that stratification of children's cohorts based on settler types may reveal group effects that might otherwise be masked., Competing Interests: "I have read the journal's policy and the authors of this manuscript have the following competing interests: AEB and PHMS have proprietary rights to the IS-pro technique and are co-owners of the spin-off company IS-Diagnostics. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

The allicin diallyldisulfid- S -oxide, a major garlic organosulfur compound (OSC) in crushed garlic ( Allium sativum L.), possesses antibacterial effects, and influences gut bacteria. In this study, we made allicin-free garlic (AFG) extract and investigated its effects on gut microbiome. C57BL/6N male mice were randomly divided into 6 groups and fed normal diet (ND) and high-fat diet (HFD) supplemented with or without AFG in concentrations of 1% and 5% for 11 weeks. The genomic DNAs of feces were used to identify the gut microbiome by sequencing 16S rRNA genes. The results revealed that the ratio of p- Firmicutes to p- Bacteroidetes increased by aging and HFD was reduced by AFG. In particular, the f- Lachnospiraceae , g- Akkermansia , and g- Lactobacillus decreased by aging and HFD was enhanced by AFG. The g- Dorea increased by aging and HFD decreased by AFG. In addition, the ratio of glutamic-pyruvic transaminase to glutamic-oxaloacetic transaminase (GPT/GOT) in serum was significantly increased in the HFD group and decreased by AFG. In summary, our data demonstrated that dietary intervention with AFG is a potential way to balance the gut microbiome disturbed by a high-fat diet.

Strain F21 T , a marine, aerobic, Gram-negative, rod-shaped bacterium, was isolated from seashore sand sampled in Pohang, Republic of Korea. Cells of strain F21 T were non-motile, catalase-positive, oxidase-positive, non-spore-forming and formed pinkish-red colonies on marine agar. The strain grew optimally at 37°C, pH 7 and in the presence of 2-3 % NaCl (w/v). Analysis of the 16S rRNA gene sequence of strain F21 T revealed that it belonged to the genus Algoriphagus , family Cyclobacteriaceae , with similarity values of 98.1 and 96.8 % to Algoriphagus marincola DSM 16067 T and Algoriphagus ornithinivorans IMSNU 14014 T , respectively. When comparing the genome sequence of F21 T with those of the type strains of six species of the genus Algoriphagus , the values obtained were below the thresholds for analyses of average nucleotide identity (71.8-92.7 %) and in silico DNA-DNA hybridization using the Genome-to-Genome Distance Calculator (14.7-75.2 %). The DNA G+C content of strain F21 T was 42.0 mol%. The chemotaxonomic characteristics of F21 T included MK-7 as the predominant isoprenoid quinone, iso-C 15 : 0 , iso-C 17 : 0 3-OH and summed feature 3 (C 16 : 1 ω6 c and/or C 16 : 1 ω7 c ) as major cellular fatty acids, and phosphatidylcholine and phosphatidylethanolamine as major polar lipids. On the basis of phenotypic and chemotaxonomic properties, phylogenetic distinctiveness, and genomic data, we named strain F21 T as Algoriphagus aquimaris sp. nov. and proposed that strain F21 T (=KEMB 2250-007 T = KCTC 72106 T =JCM 33187 T ) in the genus Algoriphagus represents a novel species.

Background: Significant alterations of the cutaneous microbiota (CM) have been recently demonstrated in bullous pemphigoid (BP). Microbiome data of both oral cavity (OM) and gut (GM) from patients affected by bullous disease are not available yet and, further consistent studies focused on the role of such microbial populations are still missing., Objective: Objective: In this pilot study we characterized and compared GM, OM and CM of patients affected by pemphigus vulgaris (PV) and BP to investigate a distinctive microbiome composition in this two rare dermatological disorders., Methods: High-throughput sequencing of the V1-V3 hyper-variable regions of 16S rRNA was used to compare the bacterial community composition of stool, skin and oral mucosae swabs in a cohort of PV and BP patients. A dedicated bioinformatics software coupled with in-house pipeline was implemented to analyse and compare diseases dataset., Results: GM samples of both PV and BP patients were principally characterized by Firmicutes and Bacteroidetes phyla. Interestingly, the Firmicutes phylum and Staphylococcus genus were mainly represented in cutaneous samples. The diversity of phyla in oral mucosae was higher than those of gut and skin samples and, Bacteroidetes phylum was significantly underrepresented in all PV samples., Conclusion: Firmicutes phylum and Staphilococcus genus were the most represented in OM and CM swabs of PV and BP microbial populations. Moreover, we argue the quantitative imbalance linked to the decrease of Bacteriodetes in the oral cavity of PV patients might be associated to disease typical fetor. To shed light on this peculiar feature further studies are still required., Competing Interests: Declaration of Competing Interest The authors declare no conflict of interest., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Aim: The aim of this study was to determine and compare the levels of both Bacteroidetes and Firmicutes in the gut microbiota and TLR2/TLR4 gene expression in the blood of patients with type 1 diabetes mellitus (T1DM) and healthy individuals. These results may serve as a preliminary assessment to guide future research., Method: Between January and October 2014, stool and blood samples were collected from 53 adult T1DM patients and 53 age- and gender-matched healthy individuals. Bacteroidetes and Firmicutes levels were assessed from stool sample DNA and TLR2 and TLR4 expression levels were analyzed via qPCR using RNA from EDTA blood samples from both patients and healthy controls., Results: The amounts of Bacteroidetes and Firmicutes were statistically significantly higher and lower, respectively, in the T1DM group than in the healthy control group (p < 0.001 and p < 0.001, respectively). In addition, the Firmicutes/Bacteroidetes ratios in patients with T1DM were significantly lower than in healthy controls. The TLR4 and TLR2 gene expression levels in T1DM patients were significantly upregulated and downregulated, respectively, compared to those in the control group., Conclusion: Our data are the first to show a relationship between T1DM and gut microbiota in our country. In addition, our results provide information about the connections between T1DM, gut microbiota, and TLR2 and TLR4 expression. We believe that Bacteroidetes and Firmicutes in the gut microbiota may play a role in the autoimmune process of T1DM and that these findings should be further investigated in the future., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Objectives: To summarize the literature on the influence of exercise on the gut microbiota of healthy adults., Methods: A systematic and comprehensive search in electronic database, including SciELO, Scopus, PubMed, and Web of Science up to July 5, 2019. Eligibility criterion was original studies conducted on healthy humans including exercise interventions or interventions involving any type of physical activity., Results: The initial search retrieved 619 articles of which 18 met the inclusion criteria, 9 were observational, 4 reported very short-term exercise interventions, and 5 reported medium/long-term exercise interventions. Higher levels of physical activity or cardiorespiratory fitness were positively associated with fecal bacterial alpha diversity. Contrasting associations were detected between both the level of physical activity and cardiorespiratory fitness and fecal counts for the phyla Firmicutes, Bacteroidetes, and Proteobacteria. Higher levels of physical activity and cardiorespiratory fitness were positively associated with the fecal concentration of short-chain fatty acids. Reports on the effects of very short-term and medium/long-term exercise interventions on the composition of the gut microbiota were inconsistent., Discussion: Higher levels of physical activity and cardiorespiratory fitness are associated with higher fecal bacterial alpha diversity and with the increased representation of some phyla and certain short-chain fatty acids in the feces of healthy adults. Very short-term and medium/long-term exercise interventions seem to influence the fecal counts of some phyla. However, the heterogeneity between studies hampers any strong conclusions from being drawn. Better-designed studies are needed to unravel the possible mechanisms through which exercise might influence the composition and activity of the human gut microbiota.

A Gram-stain-negative, rod-shaped, non-motile, facultatively anaerobic bacterium, designated FJ4-8 T , was isolated from a rotten hemp rope in Chongqing City, PR China. Phylogenetic analysis of 16S rRNA gene sequences indicated that the isolate was closely related to members of the family Sphingobacteriaceae, with the highest similarity to Pedobacter tournemirensis TF5-37.2-LB10 T (95.3%) and low similarities to all other species of the genus Pedobacter (90.4-93.9%). Phylogenetic analyses demonstrated that strain FJ4-8 T formed a stable subclade with Pedobacter tournemirensis TF5-37.2-LB10 T . The clade with these two strains branched adjacent to a clade containing three species of the genus Arcticibacter. MK-7 was detected as the only respiratory quinone. The major fatty acids composed iso-C 15:0 , iso-C 17:0 3-OH and summed feature three. Phosphatidylethanolamine, three aminophospholipids and one unidentified lipid were found as the major polar lipids. The major polyamine was identified as sym-homospermidine. The DNA-DNA hybridization value between strain FJ4-8 T and Pedobacter tournemirensis TF5-37.2-LB10 T was 42.0 ± 2.5%. Based on its phylogenetic, chemotaxonomic and phenotypic characteristics, the novel strain and TF5-37.2-LB10 T were found to be different from members of genera Pedobacter and Arcticibacter. FJ4-8 T and TF5-37.2-LB10 T represented different species. Therefore, FJ4-8 T should be classified as a novel species of a novel genus in the family Sphingobacteriaceae, for which the name Pararcticibacter amylolyticus gen. nov., sp. nov. is proposed. The type strain is FJ4-8 T (= KCTC 62640 T  = CCTCC AB 2018052 T ). The draft genome sequence is 6290, 449 bp in length, the genomic DNA G+C content was 44.4 mol%. Pedobacter tournemirensis TF5-37.2-LB10 T should be transferred to the novel genus as Pararcticibacter tournemirensis comb. nov. (The type strain is TF5-37.2-LB10 T (= DSM 23085 T  = CIP 110085 T  = MOLA 820 T ).

A novel strain, HME-24 T , was isolated from herbicide bensulfuron-methyl-contaminated soil in Jiangning District, Jiangsu Province, China. Strain HME-24 T was a Gram-stain-negative, strictly aerobic, non-motile and rod-shaped bacterium, and the colonies on R2A agar are yellow. The strain was non-sporulating, catalase- and oxidase-positive. Cells growth occurred at 15-37 °C (optimum, 30 °C), at pH 6.0-8.0 (optimum, 7.0) and with 0-1.5% (w/v) NaCl (optimum, 0.5% NaCl). Strain HME-24 T showed the highest 16S rRNA gene sequence identity to Edaphocola aurantiacus H2 T (99.58%), followed by Taibaiella chishuiensis AY17 T (94.02%). The sole respiratory quinone was Menaquinone-7 (MK-7), the major polar lipids of strain HME-24 T were two unidentified lipids, two unidentified aminolipids, an unidentified glycolipid and phosphatidylethanolamine, and the major fatty acids were iso-C 15:0 , iso-C 15:1 G and iso-C 17:0 3-OH. The genomic DNA G+C content values based on total genome sequences of strain HME-24 T and H2 T were 43.6 mol% and 43.8 mol%, respectively. Average nucleotide identity (ANI) for draft genomes between strain HME-24 T and H2 T was 94.8%, and the digital DNA-DNA hybridization (dDDH) for draft genomes between strain HME-24 T and H2 T was 59.2%. On the basis of phenotypic, genotypic and phylogenetic analysis, strain HME-24 T represents a novel species of the genus Edaphocola, with the name Edaphocola flava sp. nov. being proposed. The type strain of Edaphocola flava is HME-24 T (= KCTC 62977 T  = CGMCC 1.13935 T ).

An isolate, designated TTM-7 T , recovered from a freshwater river in Taiwan, was characterized using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set (92 protein clusters) indicated that strain TTM-7 T is affiliated with species in the genus Lacibacter . Strain TTM-7 T was most closely related to Lacibacter cauensis NJ-8 T with a 98.2 % 16S rRNA gene sequence similarity, followed by Lacibacter daechungensis H32-4 T (97.4 %) and Lacibacter nakdongensis SS2-56 T (96.3 %). Cells were Gram-stain-negative, aerobic, motile by gliding, rod-shaped and formed orange colonies. Optimal growth occurred at 25 °C, pH 7 and 0 % NaCl. The major fatty acids of strain TTM-7 T were iso-C 15 : 0 , summed feature 3 (comprising C 16 : 1 ω 7 c/C 16 : 1 ω 6c and/or iso-C 15 : 0 2-OH) and iso-C 15 : 1 G. The predominant hydroxy fatty acid was iso-C 17 : 0 3-OH. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, two unidentified aminoglycolipids, five unidentified aminophospholipids and one unidentified lipid. The major isoprenoid quinone was MK-7. Genomic DNA G+C content of strain TTM-7 T was 40.6 mol%. Strain TTM-7 T showed 83.6 % average nucleotide identity and 16.0 % digital DNA-DNA hybridization identity with Lacibacter cauensis NJ-8 T . On the basis of phenotypic and genotypic properties and phylogenetic inference, strain TTM-7 T should be classified in a novel species of the genus Lacibacter , for which the name Lacibacter luteus sp. nov. is proposed. The type strain is TTM-7 T (=BCRC 81159 T =LMG 30926 T =KCTC 62870 T ).

A moderately thermophilic and heterotrophic bacterial strain, LA T , was isolated from microbial mats sampled at a hot spring in Nakabusa, Nagano, Japan. The cells of strain LA T were aerobic, Gram-stain-negative, non-sporulating, non-motile and rod-shaped (2.0-4.1 µm long). The formation of dense cell aggregates in liquid medium was a unique characteristic of the strain. Strain LA T grew optimally at 50°C and at pH 7.5. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the nearest neighbour of strain LA T was Schleiferia thermophila JCM 30197 T with 94.1 % sequence similarity. The draft genome sequence of strain LA T (2 671 880 bp) showed 18.0 % digital DNA-DNA hybridization, 70.9 % average nucleotide identity and 72.1 % average amino acid identity (AAI) values in comparison with the genome sequence of S. thermophila JCM 30197 T (2 606 763 bp); the 16S rRNA gene sequence similarity and AAI values are lower than the cutoffs used for assignment to a separate genus. On the basis of phenotypic features, major cellular fatty acid composition, genome sequencing and phylogenetic position, a novel genus and species are proposed for strain LA T , to be named Thermaurantimonas aggr egans (= JCM 31826 T =DSM 106522 T ).

Aim: To identify intestinal microbiota compositions in elderly functional constipation (FC) patients. Materials & methods: Fecal samples from 61 FC patients and 48 healthy age-matched volunteers were analyzed through 16S rRNA gene sequencing. Results: The intestinal microbiota compositions of FC patients were significantly different from healthy controls. Additionally, the species diversity of healthy controls was greater than that of FC patients. Indeed, the abundance of Firmicutes and Proteobacteria was significantly decreased, whereas that of Bacteroides , Prevotella , Lactococcus , Ruminococcus and Butyricimonas was remarkably increased in FC patients. Conclusion: Elderly FC patients appear to have a unique intestinal microbiota profile. Our findings should provide insight regarding the pathogenic mechanism of FC and evidence for exploring new therapeutic strategies in elderly FC patients.

Background: The presence of the human lung microbiota has been demonstrated in patients with different lung diseases, mainly in sputum samples. However, for study of the alveolar microbiota, a bronchoalveolar lavage (BAL) sample represents the lower respiratory tract (LRT) environment. It is currently unknown whether there is a specific alveolar microbiota profile in human lung diseases, such as pulmonary tuberculosis (TB) and interstitial pneumonia (IP)., Methods: BAL samples from six active TB patients, six IP patients and ten healthy volunteers were used for DNA extraction followed by amplification of the complete bacterial 16S ribosomal RNA gene (16S rDNA). The 16S rDNA was sequenced with a MiSeq Desktop Sequencer, and the data were analysed by QIIME software for taxonomic assignment., Results: The alveolar microbiota in TB and IP patients and healthy volunteers was characterized by six dominant phyla, Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Fusobacteria and Cyanobacteria. A significant reduction in the abundance of Firmicutes was observed in IP patients. In TB and IP patients, the diversity of the alveolar microbiota was diminished, characterized by a significant reduction in the abundance of the Streptococcus genus and associated with increased Mycobacterium abundance in TB patients and diminished Acinetobacter abundance in IP patients with respect to their abundances in healthy volunteers. However, an important difference was observed between TB and IP patients: the Fusobacterium abundance was significantly reduced in TB patients. Exclusive genera that were less abundant in patients than in healthy volunteers were characterized for each study group., Conclusions: This study shows that the alveolar microbiota profile in BAL samples from TB and IP patients, representing infectious and non-infectious lung diseases, respectively, is characterized by decreased diversity., Competing Interests: Declaration of competing interest None of the authors have any competing interests., (Published by Elsevier Ltd.)

This study aimed to investigate the influences of mercuric chloride (HgCl 2 , 250 ppm, drink water) on the growth performance, cecal morphology and microbiota of chickens (n = 60) after 30, 60, and 90 days of exposure. A control group of sixty chickens received water free of HgCl 2 . Our results suggested that mercury exposure reduced the body weight and changed the cecal morphology of chickens after the 90-day treatment. Furthermore, sequence analysis of 16 S rRNA gene revealed that the diversity and composition of cecal microbiota in chickens differed between the control and exposure group. At the phylum level, Proteobacteria and Tenericutes phyla both significantly increased in mercury exposure groups on day 30 while only Tenericutes phyla significantly increased on day 60. At the genus level, we observed that the change in microbial populations are most dramatic on day 30. Besides, compared with the control group, the genus Prevotellaceae&#95;UCG-001 significantly increased in exposure group on day 30 but showed no significant difference on day 60, whereas there was a significant decrease on day 90. PICRUSt analysis revealed potential metabolic changes, such as Bacterial invasion of epithelial cells and Metabolism of xenobiotics, associated with mercury exposure in chickens. Taken together, the data show that subchronic exposure to mercury not only affected the growth and development but also caused the dysbiosis of gut microbiota, which may further induced metabolic disorders in chickens., (Copyright © 2019 Elsevier Inc. All rights reserved.)

In a pioneering study, Zaura et al. (2009) found that majority of oral microbes fall within the five phyla including, Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes and Fusobacteria. Subsequent studies further identified a set of microbes that were commonly shared among unrelated individuals (i.e., core). However, these existing studies may have not been designed to investigate the interactions among various core species. Here by harnessing the power of ecological network analysis, we identified some important ecological guilds in the form of network clusters. In particular, we found that the strongest cluster is an alliance between Firmicutes and Bacteroidetes against Actinobacteria (FBA-guild). Within the guild, we further identified two sub-guilds, the Actinobacteria-dominant sub-guild (ASG) and Firmicutes-dominant allied with Bacteroidetes sub-guild (FBSG). Furthermore, we identified so-termed guard nodes in both sub-guilds, and their role may be to inhibit the peer sub-guild given they held competitive interactions only with the outside nodes only but held cooperative interactions only with the internal nodes, which we termed civilian nodes given that they only held cooperative interactions. We postulated that FBA-guild might be to do with protection of oral health against some opportunistic pathogens from Corynebacterium and Actinomyces, the two major genera of Actinobacteria (target of FB alliance).

OGG1-deficient (Ogg1-/-) animals display increased propensity to age-induced and diet-induced metabolic diseases, including insulin resistance and fatty liver. Since the intestinal microbiome is increasingly understood to play a role in modulating host metabolic responses, we examined gut microbial composition in Ogg1-/- mice subjected to different nutritional challenges. Interestingly, Ogg1-/- mice had a markedly altered intestinal microbiome under both control-fed and hypercaloric diet conditions. Several microbial species that were increased in Ogg1-/- animals were associated with increased energy harvest, consistent with their propensity to high-fat diet induced weight gain. In addition, several pro-inflammatory microbes were increased in Ogg1-/- mice. Consistent with this observation, Ogg1-/- mice were significantly more sensitive to intestinal inflammation induced by acute exposure to dextran sulfate sodium. Taken together, these data indicate that in addition to their proclivity to obesity and metabolic disease, Ogg1-/- mice are prone to colonic inflammation. Further, these data point to alterations in the intestinal microbiome as potential mediators of the metabolic and intestinal inflammatory response in Ogg1-/- mice., Competing Interests: The authors have declared that no competing interests exist.

The microbial response to environmental changes in coastal waters of the eastern Cantabrian Sea was explored for four years by analysing a broad set of environmental variables along with bacterial community metabolism and composition. A recurrent seasonal cycle emerged, consisting of two stable periods, characterized by low bacterial metabolic activity (winter) from October to March, and high bacterial metabolic activity (summer) from May to August. These two contrasting periods were linked by short transition periods in April (T A ) and September (T S ). The phylogenetic groups Alphaproteobacteria and Bacteroidetes were dominant during winter and summer respectively, and their recurrent alternation was mainly driven by the bloom of eukaryotic phytoplankton before T A and the bloom of prokaryotic phytoplankton before T S . Bacterial growth efficiency remained high and stable during the winter and summer periods but dropped during the two short transition periods. Our results suggest that bacterial growth efficiency should be considered a very resilient property that reflects different stages in the adaptation of the bacterial community composition to the environmental changes occurring throughout the seasonal cycle in this coastal ecosystem., (© 2019 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Characterizing bacterial communities is of great significance for targeted control of bacteria-induced clogging during geothermal water recharge. Based on a series of laboratory-scale percolation experiments, the variations in bacterial community diversity, composition, and structure were investigated during simulated geothermal water recharge using high-throughput sequencing technology. The Chao, Shannon, and Evenness indexes were used to quantify the richness, diversity, and evenness of the bacterial community, respectively. The results show that the richness of the bacterial community initially increased and then decreased in the sand columns during the experiments of geothermal water recharge, while the changes in bacterial diversity and evenness were not apparent. A variety of bacterial phyla were found, among which Proteobacteria was predominant (88.31%), followed by Actinobacteria, Bacteroidetes, and Firmicutes (4.23%, 3.44%, and 2.49%). For the non-Proteobacterial phyla, Actinobacteria gradually disappeared while Bacteroidetes and Firmicutes were detected during the percolation experiments. This study implies that, despite the variations in the bacterial community, a core group of bacteria persists during geothermal water recharge, and thus a targeted control of bacteria-induced clogging during geothermal water recharge should be feasible.

Three groups of Gram-stain-negative, obligately anaerobic, rod or coccoid-shaped bacteria, which were phylogenetically assigned in the genus Alistipes belonging to the family Rikenellaceae in the phylum Bacteroidetes , were isolated from the faecal samples of healthy Japanese humans. Group I (strains 5CBH24 T and 6CPBBH3) showed highest 16S rRNA gene sequence similarity to ' Alistipes obesi ' ph8 T (99.73 %). Group II (strain 5CPEGH6 T ) was related to Alistipes shahii WAL 8301 T (96.82 %). Ten strains of group III (3BBH6 T , 5CPYCFAH4, 5NYCFAH2 and others) were related to Alistipes onderdonkii DSM 19147 T (98.96 %). Group I could be differentiated from other strains by the ability to hydrolyse aesculin and the lack of catalase activity. Strain 5CPEGH6 T could be differentiated from A. shahii JCM 16773 T by the inability to hydrolyse aesculin and the lack of catalase activity, and so on. Phenotypic characteristics of group III were similar to those of A. onderdonkii JCM 16771 T . Strains 5CBH24 T , 6CPBBH3 and ' A. obesi ' ph8 T shared 98.8-98.9 % average nucleotide identity (ANI) with each other. In addition, the in silico DNA-DNA hybridization (DDH) values among three strains were 86.7-89.4 %. Strain 5CPEGH6 T showed relatively low values (≤ 84.4 % for ANI ; ≤26.2 % for DDH) with other strains. Three strains in the group III (3BBH6 T , 5CPYCFAH4 and 5NYCFAH2) shared 97.9-99.9% ANI with each other. These three strains showed 96.9-97.3 % ANI with A. onderdonkii DSM 19147 T . The DDH values of strains 3BBH6 T , 5CPYCFAH4 and 5NYCFAH2 among themselves were 80.5-99.8 %, while those compared to A. onderdonkii DSM 19147 T were 71.0-73.4 %. On the basis of the collected data, three novel species, Alistipes communis sp. nov. (5CBH24 T =JCM 32850 T =DSM 108979 T ), Alistipes dispar sp. nov. (5CPEGH6 T =JCM 32848 T =DSM 108978 T ) and Alistipes onderdonkii subsp. vulgaris subsp. nov. (3BBH6 T =JCM 32839 T =DSM 108977 T ), are proposed.

A bacterial strain designated 5GH32-13 T was isolated from greenhouse soil in Yongin-city, Republic of Korea. Cells were Gram-stain-negative, strictly aerobic, motile rods of two different shapes. The strain was catalase-positive and oxidasenegative. Flexirubin-like pigments were not detected. β-Carotene was produced. The strain grew in the range of 10-37°C (optimum of 28-30°C) and pH 6-8 (optimum of pH 7) and tolerated up to 1% (w/v) NaCl (optimum of 0%). According to the 16S rRNA gene sequence comparison, strain 5GH32-13 T shared a sequence similarity of less than 96.0% with all validly named taxa, having the highest sequence similarity with Pseudoflavitalea soli KIS20-3 T (95.8%), Pseudoflavitalea rhizosphaerae T16R-265 T (95.4%), Flavitalea gansuensis JCN-23 T (95.3%), Pseudobacter ginsenosidimutans Gsoil 221 T (95.3%), and Flavitalea populi HY-50RT (95.2%). A phylogenetic tree showed that strain 5GH32-13 T was not grouped consistently into any specific genus. Its only polyamine was homospermidine, and its major fatty acids (> 10% of total fatty acids) were iso-C 15:0 , iso-C 17:0 3-OH, and iso-C 15:1 G. The strain's only respiratory quinone was MK-7, and its polar lipids were phosphatidylethanolamine, one unidentified phospholipid, six unidentified aminolipids and four unidentified lipids. Its DNA G + C content was 47.5 mol%. The results from chemotaxonomic, phenotypic and phylogenetic analyses indicated that strain 5GH32-13 T represents a novel species of a novel genus of the family Chitinophagaceae, and the name Paraflavitalea soli gen. nov., sp. nov. is proposed. The type strain is 5GH32-13 T (= KACC 17331 T = JCM 33061 T ).

A novel Gram-stain-negative, aerobic, rod-shaped, reddish-orange-coloured, gliding bacterial strain, designated L12M1 T , was isolated from the gut of the Korean scallop, Patinopecten yessoensis . Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain L12M1 T formed a monophyletic clade with the strains in the genus Flammeovirga and showed highest 16S rRNA gene sequence similarity to Flammeovirga kamogawensis YS10 T (98.66 %). The major cellular fatty acids of strain L12M1 T were iso-C 15 : 0 and C 20 : 4 ω6,9,12,15 c . The predominant isoprenoid quinone was MK-7. The major polyamines were spermidine, cadaverine and the minor polyamine was putrescine. The DNA G+C content was 32.1 mol%. The phylogenetic, phenotypic, biochemical, chemotaxonomic and genotypic results indicated that strain L12M1 T represents a novel species of the genus Flammeovirga , for which the name Flammeovirga pectinis sp. nov. is proposed. The type strain is L12M1 T (=KCTC 62750 T =JCM 33169 T ).

A Gram-stain-negative, aerobic, non-motile and ovoid- or rod-shaped bacterial strain, designated HSMS-39 T , was isolated from marine sand sampled at Hongsung, Republic of Korea. Strain HSMS-39 T grew optimally at 30 °C and in the presence of 1.0-2.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences showed that strain HSMS-39 T fell within the clade comprising the type strains of Lewinella species, clustering with the type strain of Lewinella marina showing 16S rRNA gene sequence similarity of 99.1 %. It exhibited 16S rRNA gene sequence similarities of less than 95.5 % to the type strains of the other Lewinella species. Strain HSMS-39 T contained MK-7 as the predominant menaquinone and iso-C 17 : 1 ω9 c , iso-C 15 : 0 and summed feature 3 (C 16 : 1 ω7 c and/or C 16 : 1 ω6 c ) as the major fatty acids. The major polar lipids of strain HSMS-39 T were phosphatidylethanolamine and one unidentified phospholipid. The DNA G+C content of strain HSMS-39 T was 60.0 mol%. The mean DNA-DNA relatedness value between strain HSMS-39 T and the type strain of L. marina was 15 %. The average nucleotide identity value between strain HSMS-39 T and the type strain of L. marina was 81.87 %. The phylogenetic and genetic data and differential phenotypic properties indicated that strain HSMS-39 T is separated from other recognized species of the genus Lewinella . On the basis of the polyphasic data, strain HSMS-39 T is considered to represent a novel species of the genus Lewinella , for which the name Lewinella litorea sp. nov. is proposed. The type strain is HSMS-39 T (=KACC 19866 T =NBRC 113585 T ).

A Gram-stain-negative, non-motile, rod-shaped, oxidase-positive, red-pigmented bacterium, strain N3 T , was isolated from Fuxian lake, a freshwater lake in Yunnan Province, PR China. Strain N3 T was facultatively anaerobic, heterotrophic and negative for catalase. Optimal growth occurred at 30 °C (range 4-45 °C), pH 7.0-8.0 (range 6.5-9.5) and in the presence of 0-3 % (w/v) NaCl (range 0-3 %). The results of phylogenetic analysis based on 16S rRNA gene sequencing revealed that strain N3 T was close to the type strains of Algoriphagus aquaeductus , Algoriphagus shivajiensis and Algoriphagus alkaliphilus with sequence similarities of 97.4, 97.3 and 97.2 % respectively. The G+C content of the genomic DNA was 43.9 mol%. The quinone system contained menaquinone MK-7 as the sole component. The major fatty acids were iso-C 15 : 0 , summed feature 9 (10-methyl C 16 : 0 and/or iso-C 17 : 1 ω 9 c ), summed feature 3 (C 16 : 1 ω 6 c and/or C 16 : 1 ω 7c ) and iso-C 16 : 0 . Major polar lipids were phosphatidylcholine, phosphatidylethanolamine, an unidentified glycolipid, one unidentified phospholipid, two unidentified aminolipids and four unidentified lipids. On the basis of physiological, chemotaxonomic and molecular properties as well as phylogenetic distinctiveness, strain N3 T should be placed into the genus Algoriphagus as a novel species, for which the name Algoriphagus lacus sp. nov. is proposed. The type strain is N3 T (=KCTC 62622 T =MCCC 1H00308 T ).

A Gram-stain-negative, rod-shaped and facultatively anaerobic strain, designated CG51 T , was isolated from marine sediment collected from a coastal area in Weihai, PR China. Strain CG51 T grew at 4-37 °C (optimum, 28-30 °C), with 1.0-6.0 % (w/v) NaCl (2.0-3.0 %) and at pH 6.0-8.5 (pH 7.0-7.5). The predominant fatty acids were iso-C 15 : 0 , anteiso-C 15 : 0 and iso-C 14 : 0 . Major polar lipids included an unidentified lipid and a phospholipid. The respiratory quinone was MK-7 and the genomic DNA G+C content was 35.9 mol%. The results of phylogenetic analysis based on 16S rRNA gene sequences placed strain CG51 T in the genus Labilibacter with the close relatives being Labilibacter marinus Y11 T and Labilibacter aurantiacus HQYD1 T , exhibiting 96.5 and 96.3 % 16S rRNA pairwise similarity, values which are clearly below the 98.7 % threshold value recommended for species demarcation. Based on the phylogenetic, physiological, chemotaxonomic and genetic data, strain CG51 T represents a novel species within the genus Labilibacter , for which the name Labilibacter sediminis sp. nov. is proposed. The type strain is CG51 T (=MCCC 1K03739 T =JCM 33138 T ).

Microbial communities in natural ecosystems are subject to strong ecological rules. The study of local communities along a regional metacommunity can reveal patterns of community assembly, and disentangle the underlying ecological processes. In particular, we seek drivers of community assembly at the regional scale using a large lacustrine dataset (>300 lakes) along the geographical, limnological and physico-chemical gradients in the Pyrenees. By using high throughput amplicon sequencing of the 16S rRNA gene, and inferring environmental sources of bacterial immigrants, we showed that surface aquatic bacterial assemblages were strongly influenced by terrestrial populations from soil, biofilms or sediments, and primarily selected by a pH-alkalinity gradient. Indeed, source proportions explained 27% of the community variation, and chemistry 15% of the total variation, half of it shared with the sources. Major taxonomic groups such as Verrucomicrobia, Actinobacteria and Bacteroidetes showed higher aquatic affinities than Parcubacteria, Gammaproteobacteria, Alphaproteobacteria or Betaproteobacteria, which may be recruited and selected through different hydrographic habitats. A regional fingerprint was observed with lower alpha diversity and higher beta diversity in the central Pyrenees than in both ends. We suggest an ecological succession process, likely influenced by complex interactions of environmental source dispersal and environmental filtering along the mountain range geography., (© 2019 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Microorganisms play important roles in soil improvement. Therefore, clarifying the contribution of environmental factors in shaping the microbial community structure is beneficial to improve soil fertility in karst rocky desertification areas. Here, the bacterial community structures of eight rhizospheric soil samples collected from perennial fruit plantations were analysed using an Illumina HiSeq2500 platform. The diversity and abundance of bacteria in rocky desertification areas were significantly lower than those in non-rocky desertification areas, while the bacterial community structure was not significantly different between root surface and non-root surface soils in the same rhizospheric soil samples. Proteobacteria predominated in rocky desertification areas, while Actinobacteria predominated in non-rocky desertification areas. Correlation analysis revealed that water-soluble phosphorus content (r 2  = 0.8258), latitude (r 2  = 0.7556), altitude (r 2  = 0.7501), and the age of fruit trees (r 2  = 0.7321) were positively correlated with the bacterial community structure, while longitude, pH, and total phosphorus content did not significantly influence the soil bacterial community structure. As water-soluble phosphorus content is derived from insoluble phosphorus minerals, supplementing phosphorus-solubilising bacteria to soils in rocky desertification areas is a feasible strategy for accelerating the dissolution of insoluble phosphorus minerals and improving agricultural production and environment ecology.

Microbial diversity in machine oil contaminated soil was determined by high-throughput amplicon sequencing technology. The diversity of culturable microbes in the contaminated soil was further characterized using polymerase chain reaction method. Proteobacteria and Bacteroidetes were the most dominant phyla and occupied 52.73 and 16.77%, respectively, while the most abundant genera were Methylotenera (21.62%) and Flavobacterium (3.06%) in the soil. In the culturable microbes, the major phyla were Firmicutes (46.15%) and Proteobacteria (37.36%) and the most abundant genera were Bacillus (42.86%) and Aeromonas (34.07%). Four isolated microbes with high machine oil degradation efficiency were selected to evaluate their characteristics on the oil degradation. All of them reached their highest oil degradation rate after 7 days of incubation. Most of them significantly increased their oil degradation rate by additional carbon or organic nitrogen source in the incubation medium. The oil degradation rate by combination of the four microbes at the same inoculation level was also higher than the rate from each individual microbe. The protocol and findings of this study are very useful for developing micro-bioremediation method to eliminate machine oil contaminants from soil., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

A Gram-stain-negative, aerobic, non-motile, rod-shaped, cold-tolerant bacterium, designated F01003 T , was isolated from soil sampled near Happiness Bay on the west coast of Antarctica. Strain F01003 T was found to grow at 4-30 °C (optimum, 25 °C), pH 5.5-8.0 (pH 6.5-7.0) and in the presence of 0-1 % NaCl (0 %, w/v). Cells were oxidase-positive and catalase-positive. Strain F01003 T contained menaquinone 7 (MK-7) as the predominant respiratory quinone. The main cellular fatty acids included summed feature 3 (C 16 : 1 ω6 c and/or C 16 : 1 ω7 c ) and iso-C 15 : 0 . Phosphatidylethanolamine and an unidentified aminolipid were identified as the major polar lipids. The DNA G+C content of strain F01003 T was 44.8 mol%. Phylogenetic analysis of the nearly full-length 16S rRNA gene sequence revealed that strain F01003 T was most closely related to the genus Mucilaginibacter and exhibited the highest sequence similarity to Mucilaginibacter phyllosphaerae LMG 29118 T (97.3 %). On the basis of the evidence presented in this polyphasic taxonomic study, strain F01003 T is considered to represent a novel species of the genus Mucilaginibacter , for which the name Mucilaginibactergilvus sp. nov. is proposed. The type strain is F01003 T (=KCTC 62991 T =CCTCC AB 2019023 T ).

Fish-associated antibiotic resistance genes (ARGs) have attracted increasing attention due to their potential risks to human beings via the food chain. However, data are scarce regarding the antibiotic resistance in fish themselves. Herein, the antibiotic resistance genes (ARGs) were assessed in the gut of four major Chinese freshwater carp (i.e., silver carp, grass carp, bighead carp, and crucian carp) from food retail markets. Results show that the abundances of target ARGs (e.g., tetA, tetO, tetQ, tetW, sulI, sulII, and bla TEM-1 ) and class 1 integrase (intI1) were in the range 9.4 × 10 -6 - 1.6 × 10 -1 and 6.7 × 10 -5 - 5.2 × 10 -2 gene copies per 16S rRNA gene, respectively. The sulI, sulII, and tetQ strongly correlated with silver and mercury resistance genes (e.g., silE and merR). The microbial taxa of fish gut could be partly separated among retail markets based on the PCA analysis. About 15.0% of the OTUs in fish gut were shared and 74.5% of the shared OTUs were identified as Acidobacteria, Bacteroidetes, Chloroflexi, Cyanobacteria, Firmicutes, and Proteobacteria. These phyla may constitute the core microbiota in the guts of the four Chinese freshwater carp. The possible ARG hosts were revealed based on the network analysis, and the presence of pathogen-associated resistant genera in fish gut highlights the need to fully understand their potential human health risks., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

A Gram-strain negative, aerobic, catalase and oxidase positive, non-motile, short rod-shaped bacterium, designated 17mud1-8 T , was isolated from mud collected from Nowon-gu, Seoul, South Korea. The strain was found to be able to grow at 10-40 °C (optimum 28-30 °C), pH 5.0-8.0 (optimum 7.0), and in the absence of NaCl. The nearly full-length 16S rRNA gene of strain 17mud1-8 T exhibits sequence similarity of 94.1% with that of Panacibacter ginsenosidivorans Gsoil 1550 T , followed by 93.6% sequence similarity with Parafilimonas terrae DSM 28286 T . Phylogenetic analysis indicated that strain 17mud1-8 T belongs to the family Chitinophagaceae, sharing approximately 94.1-91.9% sequence similarity with members of closely related genera. The respiratory quinone was identified as MK-7. The predominant fatty acids were found to consist of iso-C 15:0 , iso-C 17:1 ω5c and iso-C 15:1 G. The polar lipids were identified as phosphatidylethanolamine, an unidentified aminophospholipid, an unidentified glycolipid, ten unidentified aminolipids and seven unidentified lipids. The draft genome of 17mud1-8 T has G+C content of 40.9 mol% and a 5.8 Mb chromosome. On the basis of the phenotypic and genotypic properties, and phylogenetic inference, strain 17mud1-8 T was found to represent a novel genus in the family Chitinophagaceae, for which the name Ilyomonas limi gen. nov., sp. nov. is proposed, with the type strain 17mud1-8 T (=KCTC 52874 T = NBRC 112826 T ).

A Gram-stain-negative, non-motile bacterial strain, designated SW125 T , was isolated from a deep-sea vsediment sample collected from the Indian Ocean. Cells were aerobic, catalase-positive and oxidase-positive. The strain grew at 4-42 °C (optimum, 30 °C), at pH 5.0-10.0 (optimum, pH 7.0-7.6) and in the presence of 0.5-9.0 % (w/v) NaCl (optimum, 2.0-3.0 %). Comparative analyses of the 16S rRNA gene sequence showed that strain SW125 T was grouped in the vicinity of the genus Negadavirga with the highest sequence similarity of 91.6 % to the type strain of Negadavirga shengliensis . The quinone system contained menaquinone MK-7 as the predominant component. The predominant cellular fatty acids of strain SW125 T were iso-C 15 : 0 , iso-C 17 : 0 3-OH and summed feature 3 (comprising C 16 : 1 ω7 c and/or C 16 : 1 ω6 c ). Strain SW125 T contained phosphatidylethanolamine as the major polar lipid. The genomic DNA G+C content of strain SW125 T was 43.2 mol%. On the basis of its phenotypic characteristics and phylogenetic data, strain SW125 T represents a novel species of a new genus, for which the name Pleomorphovibrio marinus gen. nov., sp. nov. is proposed. The type strain is SW125 T (=CGMCC 1.16172 T =DSM 107180 T =KCTC 62653 T ).

Until 2010, our knowledge of the uterine microbiome in cows that developed uterine disease relied almost exclusively on culture-dependent studies and mostly included cows with clinical endometritis (i.e., with purulent uterine discharge). Those studies consistently found a strong positive correlation between Trueperella pyogenes and clinical endometritis, whereas other pathogens such as Escherichia coli, Fusobacterium necrophorum, Prevotella melaninogenica, and Bacteroides spp. were also commonly cocultured. In contrast, Streptococcus spp., Staphylococcus spp., and Bacillus spp. were usually isolated from healthy cows. Starting in 2010, culture-independent studies using PCR explored the microbiome of cows with metritis and clinical endometritis, and observed that E. coli was a pioneer pathogen that predisposed cows to infection with F. necrophorum, which was strongly associated with metritis, and to infection with T. pyogenes, which was strongly associated with clinical endometritis. Starting in 2011, culture-independent studies using metagenomic sequencing expanded our knowledge of the uterine microbiome. It has been shown that cows have bacteria in the uterus even before calving, they have an established uterine microbiome within 20 min of calving, and that the microbiome structure is identical between cows that develop metritis and healthy cows until 2 d postpartum, after which the bacterial structure of cows that developed metritis deviates in favor of greater relative abundance of Bacteroidetes and Fusobacteria and lesser relative abundance of Proteobacteria and Tenericutes. The shift in the uterine microbiome in cows that develop metritis is characterized by a loss of heterogeneity and a decrease in bacterial richness. At the genus level, Bacteroides, Porphyromonas, and Fusobacterium have the strongest association with metritis. At the species level, we observed that Bacteroides pyogenes, Porphyromonas levii, and Helcococcus ovis were potential emerging uterine pathogens. Finally, we have shown that the hematogenous route is a viable route of uterine infection with uterine pathogens. Herein, we propose that metritis is associated with a dysbiosis of the uterine microbiota characterized by decreased richness, and an increase in Bacteroidetes and Fusobacteria, particularly Bacteroides, Porphyromonas, and Fusobacterium., (Copyright © 2019 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.)

The antibacterial activity of titanium dioxide nanoparticles (TiO2 NPs) has been extensively documented and applied to food packaging or environmental protection. Ingestion of TiO2 NPs via dietary and environmental exposure may pose potential health risks by interacting with gut microbiota. We conducted an animal experiment to investigate the effects of oral exposure to TiO2 NPs on gut microbiota and gut-associated metabolism in Sprague-Dawley rats. Rats were administered with TiO2 NPs (29 ± 9 nm) orally at population-related exposure doses (0, 2, 10, 50 mg kg-1) daily for 30 days. Changes in the gut microbiota and feces metabolomics were analyzed through bioinformatics. TiO2 NPs caused significant changes of colon morphology in rats, manifested as pathological inflammatory infiltration and mitochondrial abnormalities. 16S rDNA sequencing analysis showed that the structure and composition of gut microbiota in rats were modulated after exposure to TiO2 NPs. Monitoring data demonstrated that differentially expressed bacterial strains were obtained until exposure for 14 days and 28 days, including increased L. gasseri, Turicibacter, and L. NK4A136&#95;group and decreased Veillonella. Fecal metabolomics analysis showed that 25 metabolites and the aminoacyl-tRNA biosynthesis metabolic pathway have changed significantly in exposed rats. The increased metabolites were represented by N-acetylhistamine, caprolactam, and glycerophosphocholine, and the decreased metabolites were represented by 4-methyl-5-thiazoleethanol, l-histidine, and l-ornithine. Metabolic disorders of gut microbiota and subsequently produced lipopolysaccharides (LPS) led to oxidative stress and an inflammatory response in the intestine, which was considered to be a key and primary indirect pathway for toxicity induced by oral exposure to the TiO2 NPs. In conclusion, orally ingested TiO2 NPs could induce disorders of gut microbiota and gut-associated metabolism in vivo. The indirect pathway of oxidative stress and inflammatory response, probably due to dysbiosis of gut microbiota primarily, played an important role in the mechanisms of toxicity induced by oral exposure to TiO2 NPs. This may be a common mechanism of toxicity caused by oral administration of most nanomaterials, as they usually have potential antimicrobial activity.