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Salinibacter ruber is an extremophilic bacterium able to grow in high-salts environments, such as saltern crystallizer ponds. This halophilic bacterium is red-pigmented due to the production of several carotenoids and their derivatives. Two of these pigment molecules, salinixanthin and retinal, are reported to be essential cofactors of the xanthorhodopsin, a light-driven proton pump unique to this bacterium. Here, we isolate and characterize an outer membrane porin-like protein that retains salinixanthin. The characterization by mass spectrometry identified an unknown protein whose structure, predicted by AlphaFold, consists of a 8 strands beta-barrel transmembrane organization typical of porins. The protein is found to be part of a functional network clearly involved in the outer membrane trafficking. Cryo-EM micrographs showed the shape and dimensions of a particle comparable with the ones of the predicted structure. Functional implications, with respect to the high representativity of this protein in the outer membrane fraction, are discussed considering its possible role in primary functions such as the nutrients uptake and the homeostatic balance. Finally, also a possible involvement in balancing the charge perturbation associated with the xanthorhodopsin and ATP synthase activities is considered.

Recent studies have provided compelling evidence linking the composition of the gut microbiota, host diet, and host physiology. Prebiotics are substrates that are selectively utilized by host microorganisms, conferring health benefits. Prebiotics, such as prebiotic blends (PB), are commonly used worldwide in food processing. Here, microbiome-metabolomics was used to evaluate how PB affect gut microbes and metabolic functions in C57BL/6 J mice administered cefixime. We found favorable effects of PB on obesity outcomes. PB supplementation significantly increased the abundance of Bifidobacterium, Parabacteroides, Alloprevotella, Alistipes, and Dubosiella, and decreased that of Robinsoniella, Blautia, Lachnoclostridium, Coprobacillus, Hungatella, Erysipelatoclostridium, Helicobacter, Clostridium sensu stricto 1, Enterococcus, and Akkermansia compared to that in the cefixime administration (CEF) group. In particular, PB increased the abundance of Parabacteroides goldsteinii and suppressed that of Robinsoniella peoriensis and Akkermansia muciniphila. In addition, it regulated the levels of microbial metabolites such as unsaturated fatty acids and bile acids. Thus, PB can alleviate metabolic disorders induced by antibiotic intervention, indicating a potential dietary strategy for populations with antibiotic-associated diarrhea. KEY POINTS: • Prebiotic blends significantly increased the Parabacteroides goldsteinii colony. • Prebiotic blends selectivity reversed this increase of Akkermansia muciniphila by antibiotic intervention. • Prebiotic blends relieve cefixime-induced alteration of intestinal flora by regulating metabolites, such as fatty acids and bile acids.

This prospective study was aimed to explore the bacterial diversity of marine mucilage developed in the Marmara Sea and the North Aegean Sea by metabarcoding. For this purpose, mucilage samples were collected from five different sampling locations, and the bacterial community structure was analyzed by 16S rRNA gene amplicon sequencing. The results highlighted a diverse bacterial community dominated by Proteobacteria and Bacteroidetes species. A negative and significant correlation between pH level and Campylobacterales, Clostridiales, and Vibronales abundances was detected, while a strong positive correlation was determined between total phosphorus (TP) and Campylobacterales. Results revealed that the bacterial community in the mucilage samples was predominated by particle-attached species preferring high-nutrient concentrations. This is the first study evaluating the bacterial diversity in a mucilage outbreak using a metabarcoding approach. Its results may contribute to this growing area of research and provide a database for further studies.

Contractile injection systems (CISs) are phage tail-like nanomachines, mediating bacterial cell–cell interactions as either type VI secretion systems (T6SSs) or extracellular CISs (eCISs). Bioinformatic studies uncovered a phylogenetic group of hundreds of putative CIS gene clusters that are highly diverse and widespread; however, only four systems have been characterized. Here we studied a putative CIS gene cluster in the marine bacterium Algoriphagus machipongonensis. Using an integrative approach, we show that the system is compatible with an eCIS mode of action. Our cryo-electron microscopy structure revealed several features that differ from those seen in other CISs: a ‘cap adaptor’ located at the distal end, a ‘plug’ exposed to the tube lumen, and a ‘cage’ formed by massive extensions of the baseplate. These elements are conserved in other CISs, and our genetic tools identified that they are required for assembly, cargo loading and function. Furthermore, our atomic model highlights specific evolutionary hotspots and will serve as a framework for understanding and re−engineering CISs., Nature Microbiology, 7 (3), ISSN:2058-5276

The association between gut microbiome and chronic metabolic disease including polycystic ovary syndrome (PCOS), is well documented, however, the relationship between the gut microbiota and serum metabolites remains unknown. In this study, untargeted metabolomics together with a 16S rRNA gene sequencing tool was used to detect small molecule serum metabolites and the gut microbiome. We identified 15 differential metabolites between PCOS patients and the healthy control. Lysophosphatidylcholine (LPC) (18:2, 20:3, 18:1, P-16:0, 17:0, 15:0, 18:3, 20:4), phosphatidylcholine(PC), ganglioside GA2 (d18:1/16:0) and 1-linoleoylglycerophosphocholine were increased in the PCOS group, and the concentrations of phosphoniodidous acid, bilirubin, nicotinate beta-d-ribonucleotide and citric acid were decreased in the PCOS group, suggesting a lipid metabolism and energy metabolism disorder in the PCOS patients. The diversity of gut microbiota in PCOS group was lower than that in healthy controls. Escherichia/Shigella, Alistipes and an unnamed strain 0319_6G20 belonging to Proteobacteria were important distinguishing genera (LDA > 3.5) in PCOS. Prevotella_9 was positively correlated with phosphoniodidous acid, nicotinate beta-d-ribonucleotide and citric acid concentrations, and negatively correlated with the concentration of LPC (20:3) and 1-linoleoylglycerophosphocholine; Roseburia was negatively correlated with LPC concentration (20:4), while the characteristic genus 0319_6G20 of PCOS was positively correlated with LPC concentration (20:3) (COR > 0.45). SF-36 in the PCOS group was significantly lower than that in the healthy control (HC) group, which was associated with the presence of Escherichia-Shigella and Alistipes. Our finding demonstrated the correlation between the gut microbiota and serum metabolites in PCOS, and therefore characteristic gut microbiota and metabolites may play an important role in the insulin resistance and the mood changes of PCOS patients.

Funder: University of Melbourne; doi: http://dx.doi.org/10.13039/501100001782, Funder: Baker Heart and Diabetes Institute; doi: http://dx.doi.org/10.13039/501100014643, Funder: Munz Chair of Cardiovascular Prediction and Prevention, Funder: Medical Research Council; doi: http://dx.doi.org/10.13039/501100000265, Funder: Engineering and Physical Sciences Research Council; doi: http://dx.doi.org/10.13039/501100000266, Funder: Economic and Social Research Council; doi: http://dx.doi.org/10.13039/501100000269, Funder: Department of Health and Social Care; doi: http://dx.doi.org/10.13039/501100000276, Funder: Chief Scientist Office, Scottish Government Health and Social Care Directorate; doi: http://dx.doi.org/10.13039/100014589, Funder: Health and Social Care Research and Development Division; doi: http://dx.doi.org/10.13039/501100010756, Funder: Public Health Agency; doi: http://dx.doi.org/10.13039/501100001626, Funder: British Heart Foundation; doi: http://dx.doi.org/10.13039/501100000274, Funder: Wellcome; doi: http://dx.doi.org/10.13039/100004440, Funder: State Government of Victoria; doi: http://dx.doi.org/10.13039/501100004752, Funder: Australian Research Council; doi: http://dx.doi.org/10.13039/501100000923, Varying technologies and experimental approaches used in microbiome studies often lead to irreproducible results due to unwanted technical variations. Such variations, often unaccounted for and of unknown source, may interfere with true biological signals, resulting in misleading biological conclusions. In this work, we aim to characterize the major sources of technical variations in microbiome data and demonstrate how in-silico approaches can minimize their impact. We analyzed 184 pig faecal metagenomes encompassing 21 specific combinations of deliberately introduced factors of technical and biological variations. Using the novel Removing Unwanted Variations-III-Negative Binomial (RUV-III-NB), we identified several known experimental factors, specifically storage conditions and freeze-thaw cycles, as likely major sources of unwanted variation in metagenomes. We also observed that these unwanted technical variations do not affect taxa uniformly, with freezing samples affecting taxa of class Bacteroidia the most, for example. Additionally, we benchmarked the performances of different correction methods, including ComBat, ComBat-seq, RUVg, RUVs, and RUV-III-NB. While RUV-III-NB performed consistently robust across our sensitivity and specificity metrics, most other methods did not remove unwanted variations optimally. Our analyses suggest that a careful consideration of possible technical confounders is critical during experimental design of microbiome studies, and that the inclusion of technical replicates is necessary to efficiently remove unwanted variations computationally.

Distilled grain waste (DGW) can be converted to organic fertilizer via aerobic composting process without inoculating exogenous microorganisms. To illustrate the material conversion mechanism, this study investigated the dynamic changes of bacterial community structure and metabolic function involved in DGW composting. Results showed that a significant increase in microbial community alpha diversity was observed during DGW composting. Moreover, unique community structures occurred at each composting stage. The dominant phyla were Firmicutes, Proteobacteria, Actinobacteriota, Bacteroidota, Myxococcota, and Chloroflexi, whose abundance varied according to different composting stages. Keystone microbes can be selected as biomarkers for each stage, and Microbispora, Chryseolinea, Steroidobacter, Truepera, and Luteimonas indicating compost maturity. Co-occurrence network analysis revealed a significant relationship between keystone microbes and environmental factors. The carbohydrate and amino acid metabolism were confirmed as the primary metabolic pathways by metabolic function profiles. Furthermore, nitrogen metabolism pathway analysis indicated that denitrification and NH3 volatilization induced higher nitrogen loss during DGW composting. This study can provide new understanding of the microbiota for organic matter and nitrogen conversion in the composting process of DGW.

A Gram-stain-negative, aerobic, and yellow-pigmented bacterium, designated A3-108T, was isolated from seawater of the West Pacific Ocean. Cells were non-motile and rod-shaped, with carotenoid-type pigments. Strain A3-108T grew at pH 6.0–8.5 (optimum 6.5) and 15–40 °C (optimum 28 °C), in the presence of 0.5–10% (w/v) NaCl (optimum 1.0%). It possessed the ability to produce H2S. Based on the 16S rRNA gene analysis, strain A3-108T exhibited highest similarity with Aureisphaera salina A6D-50T (90.6%). Phylogenetic analysis shown that strain A3-108T affiliated with members of the family Flavobacteriaceae and represented an independent lineage. The principal fatty acids were iso-C15:0, iso-C17:0 3-OH, iso-C15:1 G, and summed feature 3 (C16:1ω7c and/or C16:1ω6c). The sole isoprenoid quinone was MK-6. The major polar lipids were phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified aminolipid and one unidentified lipid. The ANIb, in silico DDH and AAI values among the genomes of strain A3-108T and three reference strains were 67.3–71.1%, 18.7–22.1%, and 58.8–71.4%, respectively. The G + C content was 41.0%. Distinctness of the phylogenetic position as well as differentiating chemotaxonomic and other phenotypic traits revealed that strain A3-108T represented a novel genus and species of the family Flavobacteriaceae, for which the name Luteirhabdus pelagi gen. nov., sp. nov. is proposed (type strain, A3-108T = CGMCC 1.18821T = KCTC 82563T).

Tongue squamous cell carcinoma (TSCC) is the most common oral cavity malignancy. The role of the microbial community in TSCC development and progression is unclear. In the present study, 23 patients with TSCC were recruited. Tissue DNA was extracted from cancer and paracancerous normal tissues from all participants. Next-generation 16S rDNA amplicon sequencing and functional prediction were applied for taxonomic analysis. Alpha diversity measurements using the Shannon and Simpson diversity indexes indicated a significant increase in the microbiotic diversity of cancer samples (Shannon index: P = 0.001, Simpson index: P = 0.015); otherwise, no differences were found when using observed operational taxonomic units (OTUs) and Chao1 index (observed OTUs: P = 0.261, Chao1 index: P = 0.054). The dominant phyla of the microbiota included Bacteroidetes, Proteobacteria, Firmicutes, Actinobacteria, and Fusobacteria. Multivariate analysis of variance (Adonis) and nonparametric analysis of similarities (ANOSIM) based on unweighted unifrac distances demonstrated differences in the bacterial community structure between the two groups (P = 0.001 for Adonis, P = 0.001 for ANOSIM). Compared with the normal samples, Neisseria, Streptococcus, and Actinomyces levels decreased significantly in cancer samples. Co-occurrence network analysis implied that the bacterial community in cancer was more conserved than that in normal tissue. Matched-pair analysis of cancer and control samples revealed a significant alteration in the relative abundance of specific taxa. These findings will enrich our knowledge of the association between the oral microbial community and TSCC. Further experiments should investigate the potential carcinogenic mechanism of microbial community alterations in TSCC. • Microbial community role in tongue squamous cell carcinoma. • Significant alteration of microbiome found between cancer and normal tissues. • Microbial community alteration and potential carcinogenic mechanism.

Pancreatic cancer is a lethal cancer with aggressive and invasive characteristics. By the time it is diagnosed, patients already have tumors extended to other organs and show extremely low survival rates. The gut microbiome is known to be associated with many diseases and its imbalance affects the pathogenesis of pancreatic cancer. In this study, we established an orthotopic, patient-derived xenograft model to identify how the gut microbiome is linked to pancreatic ductal adenocarcinoma (PDAC). Using the 16S rDNA metagenomic sequencing, we revealed that the levels of Alistipes onderdonkii and Roseburia hominis decreased in the gut microbiome of the PDAC model. To explore the crosstalk between the two bacteria and PDAC cells, we collected the supernatant of the bacteria or cancer cell culture medium and treated it in a cross manner. While the cancer cell medium did not affect bacterial growth, we observed that the A. onderdonkii medium suppressed the growth of the pancreatic primary cancer cells. Using the bromodeoxyuridine/7-amino-actinomycin D (BrdU/7-AAD) staining assay, we confirmed that the A. onderdonkii medium inhibited the proliferation of the pancreatic primary cancer cells. Furthermore, RNA-seq analysis revealed that the A. onderdonkii medium induced unique transcriptomic alterations in the PDAC cells, compared to the normal pancreatic cells. Altogether, our data suggest that the reduction in the A. onderdonkii in the gut microbiome provides a proliferation advantage to the pancreatic cancer cells. KEY POINTS: • Metagenome analysis of pancreatic cancer model reveals A. onderdonkii downregulation. • A. onderdonkii culture supernatant suppressed the proliferation of pancreatic cancer cells. • RNA seq data reveals typical gene expression changes induced by A. onderdonkii.

The rod-shaped and Gram-stain-negative bacterial strain 16FT, isolated from an air sample collected at King George Island, maritime Antarctica, was investigated to determine its taxonomic status. Strain 16FT is strictly aerobic, catalase positive, oxidase positive and non-motile. Strain 16FT hydrolyses casein, lecithin, Tween 20, 60 and 80, but not aesculin, gelatin and starch. Growth of strain 16FT is observed at 0–20 °C (optimum 10 °C), pH 5.0–8.0 (optimum pH 6.0), and in the presence of 0–2.0% NaCl (optimum 0.5%). The predominant menaquinone is MK-6, and the major fatty acids comprise anteiso-C15:0 and iso-C15:0. The major polar lipids are phosphatidylethanolamine, ornithine lipid OL2, unidentified phospholipid PL1 and the unidentified lipids L3 and L6 lacking functional groups. The DNA G + C content based on the draft genome sequence is 32.3 mol%. Sequence analysis of the 16S rRNA gene indicates the highest similarity to Kaistella palustris 3A10T (95.4%), Kaistella chaponensis Sa 1147-06 T (95.2%), Kaistella antarctica AT1013T (95.1%), Kaistella carnis NCTC 13525 T (95.1%) and below 95.0% to other species with validly published names. Phylogenetic analysis based on 16S rRNA gene and whole-genome sequences places strain 16FT in a distinct branch, indicating a separate lineage within the family Weeksellaceae. Based on the data from our polyphasic approach, 16FT represents a novel species of a new genus, for which the name Frigoriflavimonas asaccharolytica gen. nov, sp. nov. is proposed. The type strain is 16FT (= CCM 8975 T = CGMCC No.1.16844 T).

Stonebrood is a virulent disease afflicting honey bee colonies. Bacterial strains present in the gut of the Egyptian honeybee, Apis mellifera were isolated, identified and characterized. Moreover, its inhibitory effect against the etiological agent of Stonebrood disease was determined according to their antifungal activity. Both Gram-positive and Gram-negative bacteria were observed in all seasons. The spring season was found to possesses the highest abundance and variety of these bacteria. A total of 93 bacterial isolates from honeybee gut microbiota were identified by Vitek Ms method elucidating that bacterial populations in the gut of the Egyptian honeybee consist of, Firmicutes phyla (75.2%), Bacteroidetes (3.22%), Alpha-Proteobacteria (1.07%) and Gamma-Proteobacteria (20.4%). In vitro antifungal activity was carried out to determine the ability of Cell-Free Supernatants (CFS) to inhibit two Aspergillus sp., the causal agent of the Stonebrood disease. Out of 93 isolates, three of them exhibited potent antifungal activity against Aspergillus niger and A. flavus. Most antagonistic CFS identifications were performed by 16S rRNA gene sequence analysis revealing that bacterial isolates belong to Sphingomonas paucimobilis, Staphylococcus aureus, Pseudomonas aeruginosa and Lactobacillus kunkeei. Bacterial isolates obtained in this study may be potential candidates as biological control agents against Aspergillus sp.

Sea cucumbers play an important role in sediment bioturbation in coral reef and rocky intertidal ecosystems, and bacteria were a commonly-reported component of holothuroid diets. Bacterial community composition in the foregut and hindgut of two common tropical sea cucumbers (Holothuria atra and H. leucospilota) and the ambient surface sediment were investigated using high throughput sequencing based on 16S rRNA gene analysis. A total of 5 584 operational taxonomic units (OTUs) were obtained from 25 samples based on a 97% threshold, and more than half of the OTUs (n=3 694, 66.2%) were shared by the gut contents of two species of sea cucumbers and surrounding sediments. Bacterial richness and diversity in sediment samples were significantly higher than those in the gut content samples (P

The dietary supplementation of prebiotics is considered a promising strategy for the modulation of gut microbiota. Due to the wide variety of animal models and tremendous inter-individual variability from human investigations, the prebiotic effect of fibers is often difficult to compare between studies. Here, the effects of 11 dietary fibers on human fecal microbiota were studied using an in vitro human fecal fermentation model under well-controlled conditions. All fibers showed positive regulatory effects on short chain fatty acids (SCFAs) and several beneficial bacteria, including Parabacteroides distasonis and Bifidobacterium spp. Cultures supplemented with xylo-oligosaccharide and konjac flour showed the highest SCFAs. According to regulatory effects, fibers were divided into three groups, with 13 indicator OTUs (operational taxonomic units) identified. Fecal microbiota regulated by isomalto-oligosaccharide and chitosan-oligosaccharide were similar to fructo-oligosaccharide and inulin outputs. As a supplement to in vivo studies, our results comprehensively summarized the similarities and distinctiveness of fibers in regulating fecal microbiota structures. KEY POINTS: • Fibers were divided into three groups based on the regulatory effects in microbiota. • Thirteen indicator OTUs were identified using pairwise comparisons. • Fiber similarities and distinctive traits in regulating microbiota effect were identified.

A novel gram-negative, aerobic, pink, motile, gliding, rod-shaped bacterium, designated P51T, was isolated from saline silt samples in Yantai, China. It was able to grow at 4–42 °C (optimum 33 °C), pH 4.0–9.0 (optimum 7.0), and in 0–11.0% NaCl (optimum 4.0%, w/v). It grew at 4 °C, which was lower than the minimum temperature for related strains. The genome consisted of 4111 genes with a total length of 5 139 782 bp. The 16S rRNA gene sequence analysis indicated that strain P51T was a member of the genus Echinicola and most closely related to ‘Echinicola shivajiensis’. A genome analysis identified genes encoding proteins associated with carbon source utilisation, and the carotenoid biosynthesis and β-lactam resistance pathways. Strain P51T shared an average nucleotide identity value below 84.7%, an average amino acid identity value between 70.8 and 89.3%, and a digital DNA-DNA hybridisation identity of between 17.9–28.2% with closely related type strains within the genus Echinicola. The sole menaquinone was MK-7, and the major fatty acids were iso-C15:0, summed feature 3 (C16:1ω7c and/or C16:1ω6c), summed feature 4 (anteiso-C17:1 B and/or iso-C17:1 I), and summed feature 9 (iso-C17:1ω9c and/or 10-methyl C16:0). The polar lipids included one phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified phospholipid, three unidentified aminolipids, and one unknown lipid. The phenotypic, chemotaxonomic, and phylogenetic analyses suggest that strain P51T is a novel species of the genus Echinicola, for which the name Echinicola salinicaeni sp. nov. is proposed. The type strain was P51T (KCTC 82513T = MCCC 1K04413T).

An ammonia stress experiment was conducted by adjusting the concentration of total ammonia nitrogen (TAN) to 20 mg/L using ammonium chloride. The shrimp without ammonia stress was set as the control group. A total of 300 shrimp were randomly divided into six circular fiberglass tanks, each tank containing 50 shrimp. Antioxidant and immunological enzyme activities were investigated at five time points: 0 h, 12 h, 24 h, 48 h, and 96 h. The shrimp sampled at the initial time point were set as the control group. The samples used for intestinal microbiota determination were taken at two time points: 0 h and 96 h. All of the enzyme activities showed an initial increase followed by a decreasing trend. The enzyme activities (SOD, CAT, LZM, ACP, AKP) generally were higher at 12 h and 24 h compared to the control group, and then decreased some at 48 h and 96 h. The richness and diversity of intestinal microbiota decreased under ammonia stress. Proteobacteria, Firmicutes, and Bacteroidetes dominated in both the control and the 96-h group. Principal component analysis indicated a relatively small alteration of the microbiota by ammonia. Chitinophagaceae and Chloroflexi were the main species in the 96-h group, while Clostridium sensu stricto 1 and Paracoccus were the main species in the control group. Our findings suggest that ammonia exposure suppressed the antioxidant and immunological defenses of Litopenaeus vannamei. Ammonia exposure induced variation in the expression of intestinal microbiota abundance and composition, but the changes were unremarkable.

Gut microbiota dysbiosis is already a global problem after antibiotic overuse. This study was to investigate the therapeutic effect of lentinan and the mechanism of recovery of intestinal inflammation on broad-spectrum antibiotic-driven gut microbial dysbiosis in mice. Gut microbiota was elucidated by the Illumina MiSeq platform. Gas chromatography/mass spectrometry was used to investigate short-chain fatty acid content. Colon histology, expression of tight-junction associated proteins and pro-inflammatory cytokines levels were evaluated. The results showed that the gut microbiota of diversity and richness were reduced and various taxonomic levels of the gut microbiota were perturbed after antibiotics gavage. The abundance of Firmicutes and Bacteroidetes shifted to Proteobacteria and increased the relative abundance of harmful microbiota (Parabacteroides and Klebsiella) post-antibiotics, whereas lentinan administration reversed the dysbiosis and increased beneficial microbiota, including S24-7, Lactobacillus, Oscillospira, Ruminococcus and Allobaculum. The concentrations of propionic acid and butyric acid were significantly increased by treatment with lentinan. And lentinan improved colon tissue morphology and reduced pro-inflammatory cytokines via altering NF-κB signaling pathway in antibiotic-driven gut microbial dysbiosis mice. Taken together, the results proved that lentinan can be used as a prebiotic and the result provided a theoretical basis for improving the clinical treatment of broad-spectrum antibiotics side effects.

Two novel bacterial strains BT178

Background The contribution of the microbiome to pesticide breakdown in agricultural pests remains unclear. We analyzed the effect of pirimiphos-methyl (PM) on four geographically different cultures of the stored product pest mite Acarus siro (6 L, 6Tu, 6Tk and 6Z) under laboratory experiments. The effect of PM on mite mortality in the impregnated filter paper test was compared. Results The mite sensitivity to PM decreased in the order of 6 L, 6Tu, 6Tk, and 6Z. Then, the mites were cultured on PM residues (0.0125 and 1.25 µg·g−1), and population growth was compared to the control after 21 days of exposure. The comparison showed two situations: (i) increasing population growth for the most sensitive cultures (6 L and 6Tu), and (ii) no effect on mite population growth for tolerant cultures (6Z and 6Tk). The microbiome of mites was analyzed by quantification of 16S DNA copies based on quantitative polymerase chain reaction (qPCR) and by barcode sequencing of the V4 fragment of 16S DNA on samples of 30 individuals from the control and PM residues. The microbiome comprised primarily Solitalea-like organisms in all cultures, except for 6Z, followed by Bacillus, Staphylococcus, and Lactobacillus. The microbiomes of mite cultures did not change with increasing population density. The microbiome of cultures without any differences in population density showed differences in the microbiome composition. A Sodalis-like symbiont replaced Solitalea in the 1.25 µg·g−1 PM in the 6Tk culture. Sodalis and Bacillus prevailed in the microbiomes of PM-treated mites of 6Z culture, while Solitalea was almost absent. Conclusion The results showed that the microbiome of A. siro differs in composition and in response to PM residues in the diet. The results indicate that Sodalis-like symbionts can help recover mites from pesticide-induced stress.

In this study, to evaluate the effect of different biocontrol agents (BCAs) on the soil bacterial community, we investigated the effects of Bacillus amyloliquefaciens, synthetic bacterial community (Aspergillus niger:Bacillus subtilis:Bacillus licheniformis:Streptomyces microflavus = 3:3:3:1, SynCom), and BCAs combined with lime-nitrogen on soil bacterial community by utilizing 16S rRNA sequencing technology. The sequencing shows that BCAs application can improve the value of Shannon and Sobs index of bacterial community during tobacco rosette and vigorous growing period. With the growth of tobacco, the effect of BCAs on the composition and difference of soil bacterial community structure becomes more and more obvious. In terms of average relative richness, the top six phyla of soil bacterial community are Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria, Gemmatimonadetes, and Bacteroidetes. Bacillus amyloliquefaciens application can increase the relative richness of Proteobacteria and Bacteroidetes. And the combination between BCAs and lime-nitrogen can increase the relative richness of Gemmatimonadetes and Bacteroidetes. The SynCom also can increase the relative richness of Bacteroidetes, whereas it decreases the relative richness of Acidobacteria. Proteobacteria, Acidobacteria, Gemmatimonadetes, and Bacteroidetes showing an extremely significant correlation with pH and exchangeable magnesium (EMg). BCAs application can improve the tobacco yield, effective leaves, and reducing sugar content that also has extremely significant positive correlation with pH and EMg. In conclusion, the results of our field experiments clearly show that BCAs application can significantly affect the soil pH and EMg by changing most of the dominant soil bacterial species. The richness of Bacteroidetes can serve as an indicator of the changes in soil pH and EMg caused by BCAs application.

A novel bacterium, designated CAU 1574T, was isolated from marine sand. Cells were Gram stain negative, aerobic, gliding and rod shaped. Growth was observed at 20–37 °C (optimum, 30 °C), a pH of 5.5–10.0 (optimum, 8.0), and 0–3.0% (w/v) NaCl concentrations (optimum, 1%). Based on the results of 16S rRNA gene sequence analyses, strain CAU 1574T belonged to the genus Echinicola, and showed the highest similarity to Echinicola shivajiensis JCM 17847T (97.5%). Phylogenomic analysis based on consisting of 92 core genes extracted from the genome sequences showed that strain CAU 1574T was affiliated with species in the genus Echinicola. The average nucleotide identity (ANI), average amino acid identity (AAI), and digital DNA–DNA hybridization (dDDH) values between strain CAU 1574T and the closely related species were below the cut-off values of 95–96, 90, and 70%, respectively used for species demarcation. The chemotaxonomic data of CAU 1574T were as follows: major isoprenoid quinone, MK-7; predominant polar lipids, phosphatidylethanolamine, two unidentified aminophospholipids and two unidentified lipids; major fatty acids, iso-C15:0, summed feature 3 (C16:1 ω6c/C16:1 ω7c). The 5.4 Mb genome included 20 contigs and 4237 protein-coding genes with a 39.8 mol% G + C content. Based on the phylogenetic, phenotypic, and physiological result, strain CAU 1574T represents a novel species of this genus Echinicola, for which the name Echinicola arenosa sp. nov. is proposed. The type strain is CAU 1574T (= KCTC 82410T = MCCC 1K05669T).

Soy isoflavone glycoside cannot be effectively absorbed by the human intestinal tract, but probiotics with related hydrolases can transform it into aglycone to promote its absorption. In this study, a novel flavonoid-enriched yogurt was developed using an isolated β-glucosidase-producing strain (Lactiplantibacillus plantarum GY). The flavonoid aglycone-enhanced yogurt was fed to ICR mice for 21 days, and its effects were observed. The yogurt can affect the gut microbial diversity of mice, especially increasing the abundance of Parasutterella, the Bacteroidales S24-7 group, and Phascolarctobacterium in the intestinal tract of mice. Meanwhile, the ratio of Bacteroidetes/Firmicutes in the intestinal tract of mice fed with the flavonoid aglycone-enriched yogurt increased. The difference in the content of butyric acid between the L-GY + IS and the control groups was significant (P

Microorganisms are sensitive to changes in the external environment and are often used as indicators to monitor and reflect water quality. Using Illumina MiSeq sequencing, the characteristics of the microbial community in Shihou Lake water at different time points were analyzed and the key environmental factors affecting the bacterial community were identified. The microbial community diversity in Shihou Lake water was rich and showed significant differences over time. The main bacterial phyla were the Cyanobacteria, Proteobacteria, Actinobacteria, Verrucomicrobia, Bacteroidetes, Chloroflexi, Planctomycetes, Firmicutes, Chlorobi, WS6 and Saccharibacteria. The relative abundance of these major phyla in the sample accounted for 97.83%–99.07% of the total abundance; Cyanobacteria had the highest relative abundance, accounting for 13.07%–44.61% of the total, and the abundance of each dominant phylum was significantly different at different time points. The Shannon and Simpson indexes showed that the diversity of each month was as follows: August > October > July > September > November. The Chao1 and Ace indexes indicated that the order of richness was: November > October > July > August > September. Beta diversity analysis found significant differences in the samples from month to month. Environmental factors such as temperature, total nitrogen, chlorophyll-a, permanganate index, nitrite, pH and ammonia nitrogen had significant effects on microbial community structure.

Trillions of microbes harbor the gastrointestinal tract and co-exist peacefully with the human host. Microbial diversity and composition among individuals depend upon human age, diet, and environmental factors. The dynamic population of the gut microbiome, majorly consisting of Bacteroidetes and Firmicutes, forms a complex ecological community. The collective metabolic activities and interaction of gut microbiota with the host exert a marked influence on human physiology. The gut microbiota help to perform various functions, such as maintenance of intestinal mucosal integrity, production of anti-microbial peptides, protection against foreign invaders, and immunity development. In addition, they also provide essential nutrients, such as enzymes and vitamins, and also take part in metabolite synthesis, which influences both cognitive and behavioral functions of the human host. Homeostatic equilibrium among gut microorganisms, and between the microbes and intestinal interface of the host allows the maintenance of beneficial microbiota. Any alteration or dysbiosis in gut microbial composition, due to a sedentary lifestyle or intake of an unbalanced diet, plays a crucial role in the development of diseases like systemic inflammation, insulin resistance, auto-immune and metabolic disorders. This review summarizes our current understanding of the gut microbial organization, its importance in the fundamental biological processes and the pathogenesis of various human diseases and infections, and also the prognostic, diagnostic, and therapeutic potential of the gut microbiota.

A ginsenoside Rg2-producing, Gram stain-negative, aerobic, catalase and oxidase-positive, rod-shaped, non-motile and orange pigmented novel bacterium designated strain MAH-28 T was isolated from soil sample of a grape garden. Strain MAH-28 T hydrolyzed aesculin, casein and DNA. Flexirubin-type pigments are present. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain MAH-28 T formed a cluster within the genus Chitinophaga and the most close relatives were Chitinophaga alhagiae T22T (98.9% 16S rRNA gene sequence similarity), Chitinophaga humicola Ktm-2 T (98.8%), Chitinophaga barathri YLT18T (98.3%) and Chitinophaga lutea ZY74T (97.4%). The novel strain MAH-28 T has a draft genome size of 6,043,180 bp (14 contigs), annotated with 4,863 protein-coding genes, 53 tRNA and 6 rRNA genes. The ANI and dDDH values between strain MAH-28 T and the closely related type strains were in the range of 76.0–83.4% and 20.3–26.7%, respectively. The novel strain MAH-28 T was able to synthesize ginsenoside Rg2 from major ginsenoside Re. The genome annotation revealed 152 carbohydrate genes which may involve with the synthesis of ginsenoside Rg2. The respiratory quinone of strain MAH-28 T was MK-7 and the dominant cellular fatty acids were C15:0 iso, C16:1 ω5c and C17:0 iso 3-OH. The DNA G + C content of strain MAH-28 T was 53.3 mol%. Based on the phenotypic, chemotaxonomic and phylogenetic studies, strain MAH-28 T represents a new member of genus Chitinophaga for which the name Chitinophaga chungangae sp. nov. is proposed with type strain MAH-28 T (= KACC 19968 T = CGMCC 1.16605 T).

We describe here the interactions between bacterial ectosymbionts and two Caribbean mangrove crabs: Aratus pisonii (Sesarmidae) and Minuca rapax (Ocypodidae). Specimens of A. pisonii and M. rapax were collected in Guadeloupe from mangrove trees (Rhizophora mangle) and from the mangrove mud, respectively. Ectosymbionts colonizing gills in all host individuals were observed using scanning and transmission electron microscopy (SEM and TEM). No intracellular bacteria were observed in gills cells suggesting that the biofilm only occurs on the surface of the gills. For A. pisonii and M. rapax, four different bacterial morphotypes were distributed throughout the surface of gill lamellae. Different sizes and lengths were observed in the bacterial population colonizing A. pisonii and M. rapax. Either symbionts cover the entire surface of the gills, or they formed irregularly distributed patches. Molecular analyses (high-throughput amplicon sequencing of bacterial 16S rRNA-encoding genes) confirmed the occurrence of multiple bacterial taxonomic units, with dominance of Alphaproteobacteria and Bacteroidetes in both host species. However, dominant bacterial phylotypes were not shared between A. pisonii and M. rapax. This suggests that each species of these semiterrestrial crabs may harbor a specific and distinct bacterial community despite living in the same mangroves. The discussion compares the bacterial compositions of the two species and their potential functions are hypothesized. Further investigations are needed to confirm the specificity and nature of the symbiosis, including potential exchanges occurring between the partners.

Graphic abstract The research on human gut microbiome, regarded as the black box of the human body, is still at the stage of infancy as the functional properties of the complex gut microbiome have not yet been understood. Ongoing metagenomic studies have deciphered that the predominant microbial communities belong to eubacterial phyla Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria, Cyanobacteria, Verrucomicrobia and archaebacterial phylum Euryarchaeota. The indigenous commensal microbial flora prevents opportunistic pathogenic infection and play undeniable roles in digestion, metabolite and signaling molecule production and controlling host’s cellular health, immunity and neuropsychiatric behavior. Besides maintaining intestinal health via short-chain fatty acid (SCFA) production, gut microbes also aid in neuro-immuno-endocrine modulatory molecule production, immune cell differentiation and glucose and lipid metabolism. Interdependence of diet and intestinal microbial diversity suggests the effectiveness of pre- and pro-biotics in maintenance of gut and systemic health. Several companies worldwide have started potentially exploiting the microbial contribution to human health and have translated their use in disease management and therapeutic applications. The present review discusses the vast diversity of microorganisms playing intricate roles in human metabolism. The contribution of the intestinal microbiota to regulate systemic activities including gut–brain–immunity crosstalk has been focused. To the best of our knowledge, this review is the first of its kind to collate and discuss the companies worldwide translating the multi-therapeutic potential of human intestinal microbiota, based on the multi-omics studies, i.e. metagenomics and metabolomics, as ready solutions for several metabolic and systemic disorders.

We studied the microbial communities associated with the Baikal ostracods, Candona sp. (Candonidae). Bacterial biofilms were identified on the shell valves of the ostracods localized near epibiotic ciliates of the genus Lagenophrys (Ciliophora: Lagenoprydae). In situ hybridization confirmed the presence of eubacterial cells in different parts of the ostracod’s body. Bacteria of two morphotypes were detected in bacterial biofilms, including filamentous bacteria. Next-generation sequencing of 16S rRNA bacterial gene fragment allowed us to identify representatives of five bacterial phyla. Members of the phyla Proteobacteria and Bacteroidetes typical of non-marine epibiotic associations of ostracods were dominant taxa in the ostracod microbiomes. Members of other taxa (Actinobacteria, Gracilibacteria and Cyanobacteria) are likely facultative and consumed by ostracods together with detritus. In the ostracod microbiome, a significant proportion (20% of all reads) belonged to the sequences of the genus Rickettsia related to intracellular parasites.

Short-chained aliphatic polyamines (PAs) have recently been recognized as an important carbon, nitrogen, and/or energy source for marine bacterioplankton. To study the genes and taxa involved in the transformations of different PA compounds and their potential variations among marine systems, we collected surface bacterioplankton from nearshore, offshore, and open ocean stations in the Gulf of Mexico and examined their metagenomic responses to additions of single PA model compounds (putrescine, spermidine, or spermine). Genes affiliated with PA uptake and all three known PA degradation pathways, i.e., transamination, γ-glutamylation, and spermidine cleavage, were significantly enriched in most PA-treated metagenomes. In addition, identified PA-transforming taxa were mostly the alpha and gamma classes of Proteobacteria, with less important contributions from members of Betaproteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, and Planctomycetes. These findings suggest that PA transformations are ubiquitous, have diverse pathways, and are carried out by a broad range of the bacterioplankton taxa in the Gulf of Mexico. Identified PA-transforming bacterial genes and taxa were different among nearshore, offshore, and open ocean sites, but were little different among individual compound-amended metagenomes at any specific site. These observations further indicate that PA-transforming taxa and genes are site-specific and with high similarities among PA compounds. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-021-00114-x.

Two novel Gram-stain-negative, non-motile, aerobic, rod-shaped, circular, convex, red-colored and UV-tolerant strains BT594T and BT646T were isolated from soil collected in Guri city (37° 36' 0″ N, 127° 9' 0″ E) and Gwangju city (37° 22' 0″ N, 127° 17' 0″ E), respectively, South Korea. 16S rDNA sequence analysis indicated that strains BT594T and BT646T belong to a distinct lineage within the genus Hymenobacter (family Hymenobacteraceae, order Cytophagales, class Cytophagia, phylum Bacteroidetes, kingdom Bacteria). The 16S rDNA gene sequence similarity between the two strains BT594T and BT646T was 96.2%. The strain BT594T was closely related to Hymenobacter psychrotolerans Tibet-IIU11T (97.0% 16S rDNA gene similarity) and Hymenobacter tibetensis XTM003T (96.3%). The strain BT646T was closely related to Hymenobacter psychrotolerans Tibet-IIU11T (98.6%), Hymenobacter kanuolensis T-3 T (96.8%) and Hymenobacter perfusus LMG 26000 T (96.7%). The two strains were found to have the same quinone system, with MK-7 as the major respiratory quinone. The major polar lipids of strains BT594T and BT646T were phosphatidylethanolamine (PE) and aminophospholipids (APL). The major cellular fatty acids of strain BT594T were anteiso-C15:0 (17.9%), iso-C15:0 (16.1%) and summed feature 3 (C16:1 ω6c / C16:1 ω7c) (10.0%). The major cellular fatty acids of strain BT646T were summed feature 3 (C16:1 ω6c / C16:1 ω7c) (18.3%), C16:0 (17.2%) and summed feature 4 (iso-C17:1 I / anteiso-C17:1 B) (14.5%). Based on the polyphasic analysis, strains BT594T and BT646T can be suggested as two novel bacterial species within the genus Hymenobacter and the proposed names are Hymenobacter guriensis and Hymenobacter duratus, respectively. The type strain of Hymenobacter guriensis is BT594T (= KCTC 21863 T = NBRC 114853 T) and the type strain of Hymenobacter duratus is BT646T (= KCTC 21915 T = NBRC 114854 T).

The microbes associated with sponges play important roles in the nitrogen cycle of the coral reefs ecosystem, e.g., nitrification, denitrification, and nitrogen fixation. However, the whole nitrogen-cycling network has remained incomplete in any individual sponge holobiont. In this study, 454 pyrosequencing of the 16S rRNA genes revealed that the sponge Spheciospongia vesparium from the South China Sea has a unique bacterial community (including 12 bacterial phyla), dominated particularly by the genus Shewanella (order Alteromonadales). A total of 10 functional genes, nifH, amoA, narG, napA, nirK, norB, nosZ, ureC, nrfA, and gltB, were detected in the microbiome of the sponge S. vesparium by gene-targeted analysis, revealing an almost complete nitrogen-cycling network in this sponge. Particularly, bacterial urea utilization and the whole denitrification pathway were highlighted. MEGAN analysis suggests that Proteobacteria (e.g., Shewanella) and Bacteroidetes (e.g., Bizionia) are probably involved in the nitrogen cycle in the sponge S. vesparium.

Hot springs harbour diverse and interesting groups of microorganisms adapted to extreme conditions. However, due to limitations in the culture-dependent approach, most of such thermophiles remain uncultured and unexplored. Hence, this study was conducted to gain a comprehensive understanding of the bacterial diversity of Mahapelessa hot spring, Sri Lanka using both culture-dependent and culture-independent approaches. The in situ temperature of the water sample was 44.5 °C and the pH was 8.14. 16S rRNA Sanger sequencing of DNA extracted from the 18 bacterial isolates revealed the presence of eight genera belonging to two phyla: Proteobacteria (84%) and Firmicutes (16%) and the most abundant genus being Klebsiella. A total of 23 bacterial phyla representing 80 classes, 43 orders, 123 families, 205 genera and 83 species were detected by 16S rRNA V3-V4 region by amplicon metagenome sequencing of DNA extracted from water samples, where the most abundant phylum was the Proteobacteria (57.39%), followed by Firmicutes (23.7%) and Chloroflexi (4.14%). The three phyla Actinobacteria, Planctomycetes and Bacteroidetes were also detected less than 3% in abundance while 4.48% of bacteria could not be fit into any known phylum. The most abundant genera were Burkholderia (14.87%), Desulfotomaculum (7.23%) and Stenotrophomonas (6.1%). Four strictly anaerobic bacteria, Anaerosolibacter carboniphilus (0.71%), Bellilinea caldifistulae (0.04%), Salimesophilobacter vulgaris (0.1%), Anaerobacterium chartisolvens (0.12%); two potential plant growth-promoting bacteria, Azospirillum halopraeferens (0.04%) and Bradyrhizobium liaoningense (0.16%) and one potential alkali tolerant and sulphate-reducing bacterium, Desulfovibrio alkalitolerans (0.45%) were recorded. Pigmentiphaga sp. was isolated from Mahapelessa hot spring and to the best of our knowledge, this is the first record of this genus from a hot spring. This study gives insight into the vast bacterial diversity present in the Mahapelessa hot spring from the culture-independent approach which could not be identified using standard culturing techniques.

There is little knowledge about microbial functional community structures and the relationships between microbial communities and nitrogen transformation processes. Here, we investigated the relationships between soil microbial communities and nitrogen mineralisation potentials in a cool temperate forest throughout the growing season. Microbial communities were assessed by quantification of the total bacterial, archaeal, and fungal gene abundances and the bacterial and archaeal amoA gene abundances, functional predictions of bacteria and fungi, and analysis of the bacterial-fungal co-occurrence network. In mid-summer, ectomycorrhizal fungal abundance was significantly higher, whereas the total bacterial abundance was significantly lower. Bacterial and archaeal amoA gene abundances were also significantly higher in mid-summer. However, regardless of the seasonal fluctuation of microbial gene abundances, the net nitrification and nitrogen mineralisation potential did not show clear seasonality. In the network analysis, the microbial community was divided into 13 modules, which were subgroups assumed to have similar niches. Furthermore, two modules that mainly consisted of microbial species of Proteobacteria and Bacteroidetes were significantly and positively correlated with the net nitrification and mineralisation potentials. Our results indicated that microbial subgroups sharing similar niches, instead of total microbial abundances and functional gene abundances, could be important factors affecting the net nitrogen mineralisation potential.

Dissimilatory nitrate (NO3−) reduction to ammonium (DNRA) is a significant nitrogen (N) transformation process in estuarine ecosystem. The objectives of this study were to clarify the key biotic and abiotic factors influencing DNRA potential rates in Xiamen Bay. We characterized DNRA, anammox, and denitrification rates through 15 N isotope tracer experiments. Then quantitative real-time PCR and high-throughput sequencing analysis were conducted to analyze the abundance and community of DNRA bacteria. Spearman correlation analysis was used to understand the relationships of DNRA rate, nrfA abundance, and community with environmental characteristics. Denitrification was dominated in dissimilatory NO3− reduction processes in sediments of Xiamen Bay. Bacteroidetes and Proteobacteria were the main phyla of DNRA bacteria and Pelobacter was the dominant genus. Spearman correlation analysis showed that DNRA rate was significantly positively correlated with nitrite (NO2−) and NO3− in interstitial water, total organic carbon (TOC), acid volatile sulfide (AVS), and total nitrogen (TN) in sediment. Besides, nrfA abundance showed positive correlations with DNRA rate, NO2−, TOC, AVS, and TN. Furthermore, AVS and nrfA abundance were positively correlated with Pelobacter. DNRA rates were limited by sulfide, organic carbon, abundances of nrfA gene, and DNRA bacteria. Sulfide and organic carbon shaped DNRA bacterial community thereby controlled DNRA rate. Heterotrophic sulfide-producing genus (Pelobacter) prevailed among DNRA bacteria, which might support autotrophic DNRA bacteria. In this way, heterotrophic and autotrophic DNRA bacteria were connected through sulfide-producing genus and acted as a whole functional community.

Leachate generation contains a variety of toxic compounds, and is a major problem for municipal solid waste (MSW). Microbial profile knowledge is essential to new alternatives and improvements in current treatments of these effluents. In this respect, the microbial community in the leachate from the sanitary landfill of the city of Foz do Iguaçu was analyzed. The 16S rDNA metabarcoding suggested the dominance of fermenting bacteria belonging to Firmicutes phylum, followed by Proteobacteria, Bacteroidetes, and Synergistetes. The most abundant genera were Sedimentibacter, Vulcanibacillus, and Anaerovorax. However, 60% of amplicon sequence variants (ASVs) were not classified taxonomically. In addition, an expressive abundance was attributed to the superphylum known as PVC group, little studied and with unknown scientific potential. The leachate acidogenic phase was masked in the chemical and physical analyzes. Nevertheless, it was evidenced in the metabarcoding methodology. No specifically methanogenic group was detected in significant abundance. Therefore, from bacterial community identification, a bioremediation process can be designed. Enriched culture media can be developed and targeted to the recovery of specific groups which may be involved in leachate biodegradation. What is more, the results expand the knowledge of bacterial diversity, especially from the presence of unknown genera in this habitat.

Limited data exist on the spatial distribution of the colonic bacteria in humans. We collected the colonic biopsies from five segments of 27 polyp-free adults and collected feces from 13 of them. We sequenced the V4 region of the bacterial 16S rRNA gene using the MiSeq platform. The sequencing data were assigned to the amplicon sequence variant (ASV) using SILVA. Biodiversity and the relative abundance of the ASV were compared across the colonic segments and between the rectal and fecal samples. Bacterial functional capacity was assessed using Tax4fun. Each individual had a unique bacterial community composition (Weighted Bray–Curtis P value = 0.001). There were no significant differences in richness, evenness, community composition, and the taxonomic structure across the colon segments in all the samples. Firmicutes (47%), Bacteroidetes (39%), and Proteobacteria (6%) were the major phyla in all segments, followed by Verrucomicrobia, Fusobacteria, Desulfobacterota, and Actinobacteria. There were 15 genera with relative abundance > 1%, including Bacteroides, Faecalibacterium, Escherichia/Shigella, Sutterella, Akkermansia, Parabacteroides, Prevotella, Lachnoclostridium, Alistipes, Fusobacterium, Erysipelatoclostridium, and four Lachnospiraceae family members. Intra-individually, the community compositional dissimilarity was the greatest between the cecum and the rectum. There were significant differences in biodiversity and the taxonomic structure between the rectal and fecal bacteria. The bacterial community composition and structure were homogeneous across the large intestine in adults. The inter-individual variability of the bacteria was greater than inter-segment variability. The rectal and fecal bacteria differed in the community composition and structure.

In this study, fluorescence in situ hybridization (FISH) and PCR-amplified fragments of the 16SrDNA gene were used to determine prokaryotes diversity in Urmia Salt Lake. Prokaryote cell population in Urmia lake range from 3.1 ± 0.3 × 106, 2 ± 0.2 × 108, 4 ± 0.3 × 108, and 1.8 ± 0.2 × 108 cells ml−1 for water, soil, sediment, and salt samples by DAPI (4, 6-diamidino-2-phenylindole) direct count, respectively. The proportion of bacteria and archaea in the samples determinable by FISH ranged between 36.1 and 55% and 48.5 and 55.5%, respectively. According to the DGGE method, some bands were selected and separated from the gel, then amplified and sequenced. The results of sequences were related to two phyla Proteobacteria (16.6%) and Bacteroidetes (83.3%), which belonged to four genera Salinibacter, Mangroviflexus, Pseudomonas, and Cesiribacter, and the archaeal sequences were related to Euryarchaeota phyla and three genera Halonotius, Haloquadratum, and Halorubrum. According to our results, it seems that prokaryotic populations in this hypersaline environment are more diverse than expected, and bacteria are so abundant and diverse and form the metabolically active part of the microbial population inhabiting this extreme environment. Molecular dependent and independent approaches revealed a different aspect of this environment microbiota.

This case-control study explored compositions of gut microbiome in recurrent malignant gliomas patients who had received bevacizumab and Temozolomide combination treatment and Temozolomide monotherapy. We investigated gut microbiota communities in feces of 29 recurrent malignant gliomas patients received combination treatment with bevacizumab and Temozolomide (Group 1) and monotherapy with Temozolomide alone (Group 2). We took advantage of the high-throughput Illumina Miseq sequencing technology by targeting the third and fourth hypervariable (V3–V4) regions of the 16S ribosomal RNA (rRNA) gene. We found that the structures and richness of the fecal microbiota in Group 1 were different from Group 2 with LEfSe analysis. The fecal microbiota in both Group 1 and Group 2 were mainly composed by Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria. However, Group 1 patients had higher relative abundance of Firmicutes, Bacteroidetes, Actinobacteria and lower relative abundance of Bacteroidetes and Cyanobacteria in their fecal microbiota than that in Group 2 patients. To evaluate bevacizumab involved post-treatment state of the fecal microbiota profile, we used random forest predictive model and ensembled decision trees with an AUC of 0.54. This study confirmed that the gut microbiota was different in recurrent malignant gliomas patients received the combination therapy of bevacizumab and Temozolomide compared with Temozolomide monotherapy. Our discover can help better understand the influence of bevacizumab related treatment on recurrent malignant gliomas patients. Therefore, this finding may also support the potentially therapeutic options for recurrent malignant gliomas patients such as fecal microbiota transplant. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-021-00962-2.

Primary sclerosing cholangitis (PSC) is a chronic cholestatic liver disease. Its etiology remains largely unknown, although frequent concomitant inflammatory bowel disease (IBD) hints towards common factors underlying intestinal and bile duct inflammation. Herein, we aimed to explore the relative abundance of fecal microbiota in PSC-IBD patients compared to IBD-only subjects and controls. We included 14 PSC-IBD patients, 12 IBD-only patients, and 8 healthy controls (HCs). A quantitative real-time PCR (qPCR) assay was used to determine a selection of bacterial phyla, families, and genera. Relative abundance of taxa showed that Bacteroidetes was the most abundant phylum among the patients with PSC-IBD (29.46%) and also HCs (39.34%), whereas the bacterial species belonging to the phylum Firmicutes were the most frequent group in IBD-only subjects (37.61%). The relative abundance of the Enterobacteriaceae family in fecal samples of PSC-IBD patients was similar to those with IBD-only, which was significantly higher than HCs (p value = 0.031), and thus, could be used as a PSC-IBD or IBD-only associated microbial signature. Our findings showed that intestinal microbiota composition in PSC-IBD patients was completely different from that of IBD-only patients. Further studies using large-scale cohorts should be performed to better describe the contribution of the gut microbiota to PSC pathogenesis with underlying IBD.

Introduction Demodex and bacteria are both components of the ocular surface micro-ecology, constituting a complex interaction. This study aims to explore how ocular surface Demodex infestation (DI) affects ocular surface microbial communities and diversity. Methods We recruited 255 subjects, and examined the correlation between ocular surface mite infestation and clinical indicators such as age, blood glucose level, dry eye symptoms, and blood pressure. 16S rRNA sequencing was performed on the conjunctival swab samples of 14 patients with ocular DI (P group) and 17 healthy people (N group). For further analysis, the subjects were divided into four subgroups, i.e. N-NMGD (n = 11), N-MGD (n = 6), P-NMGD (n = 6), and P-MGD (n = 8), according to meibomian gland dysfunction (MGD) or no MGD (NMGD). Results There was no difference in the α-diversity of ocular surface microbial communities between the DI and healthy control groups. In linear discriminant analysis effect size (LEfSe), there were more Acinetobacter, Novosphingobium, and Anoxybacillus in the DI group and fewer Novosphingobium, Lactobacillus, and Candidatus Microthrix in the healthy control group. P-NMGD had more Thermaceae and fewer Pseudomonas than P-MGD. There were more Bacteroidetes in N-NMGD than in N-MGD. The α-diversity of P-NMGD was lower than that of N-NMGD (Shannon index, P = 0.027). At the same time, the α-diversity of N-MGD was lower than that of N-NMGD (Shannon, Simpson, and dominance index, P = 0.048). There was no significant difference in β-diversity or in the primary flora at the phylum and genus levels between groups and subgroups. Conclusion DI had no significant effect on the diversity of ocular surface microbial communities. DI primarily changed the dominant flora and relative abundance of ocular surface microbial communities. MGD may play an important role in this process.

Sedimentary environments in the Arctic are known to harbor diverse microbial communities playing a crucial role in the remineralization of organic matter and associated biogeochemical cycles. In this study, we used a combination of culture-dependent and culture-independent approaches to understanding the bacterial community composition associated with the sediments of a terrestrial versus fjord system in the Svalbard Arctic. Community-level metabolic profiling and growth response of retrieved bacterial isolates towards different carbon substrates at varying temperatures were also studied to assess the metabolic response of communities and isolates in the system. Bacterial species belonging to Cryobacterium and Psychrobacter dominated the terrestrial and fjord sediment retrievable fraction. Amplicon sequencing analysis revealed higher bacterial diversity in the terrestrial sediments (Shannon index; 8.135 and 7.935) as compared to the fjord sediments (4.5–5.37). Phylum Proteobacteria and Bacteroidetes dominated both terrestrial and fjord sediments. Phylum Verrucomicrobia and Cyanobacteria were abundant in terrestrial sediments while Epsilonbacteraeota and Fusobacteriia dominated the fjord sediments. Significant differences were observed in the carbon substrate utilization profiles between the terrestrial and fjord sediments at both 4 °C and 20 °C incubations (p

Crabs have been found to be ecologically and economically important species across various mangroves. Gut microbiota play pivotal roles in nutrient conversions, host health and pathogenicity. To understand its possible role in crab physiology and nutrient dynamics of the Indian Sundarbans, gastrointestinal tract from three crab species-Scylla serrata, Episesarama versicolor and Uca rosea, were explored for microbial community profiles using Next Generation Sequencing of V3–V4 regions of 16SrRNA gene. Based on OTU abundance, Proteobacteria was the dominant phyla, followed by Bacteroidetes, Actinobacteria, Firmicutes, Fusobacteria and Tenericutes. Vibrio, Bacillus, Lactobacillus, Corynebacterium, Spiroplasma were among the major genera. Free living soil and aquatic nutrient cycle regulators were also present. U. rosea has slightly different microbial profiles both in terms of diversity, significantly greater abundances of Actinobacteria and Nitrospira (ANOVA, P-value

A bacterial strain designated KDG-16T is isolated from a freshwater waterfall in Taiwan and characterized to determine its taxonomic affiliation. Cells of strain KDG-16T are Gram-stain-negative, strictly aerobic, motile by gliding, rod-shaped and form light yellow colonies. Optimal growth occurs at 20-25 oC, pH 6-7, and with 0% NaCl. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set reveal that strain KDG-16T is affiliated with species in the genus Flavobacterium. Analysis of 16S rRNA gene sequences shows that strain KDG-16T shares the highest similarity with Flavobacterium terrigena DSM 17934T (97.7%). The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between strain KDG-16T and the closely related Flavobacterium species are below the cut-off values of 95-96, 90 and 70%, respectively, used for species demarcation. Strain KDG-16T contains iso-C15:0, iso-C15:1 G and iso-C17:0 3-OH as the predominant fatty acids. The polar lipid profile consists of phosphatidylethanolamine, one uncharacterized aminophospholipid, one uncharacterized phospholipid, two uncharacterized aminolipids and two uncharacterized lipids. The major polyamine is homospermidine. The major isoprenoid quinone is MK-6. Genomic DNA G+C content of strain KDG-16T is 31.6%. Based on the polyphasic taxonomic data obtained, strain KDG-16T is considered to represent a novel species in the genus Flavobacterium, for which the name Flavobacterium difficile sp. nov. is proposed. The type strain is KDG-16T (=BCRC 81194T =LMG 31332T).

The first results of a study into the microbiomes of benthic invertebrates found in sites with seeps (containing methane, oil, or a combination of methane and mud) and an underwater low-temperature vent of Lake Baikal are presented. Microorganisms were detected in the intestine of an oligochaete from the cold methane seep using microscopy. Analysis of 16S rRNA gene libraries revealed that the highest diversity of microorganisms was found in the nematode microbiomes where the members of 11 phyla were identified. Some of the detected prokaryotes are methanogens, nitrifiers, and nitrogen fixators, while some are involved in the sulfur cycle. Methanotrophs were detected in the microbiomes of oligochaetes and chironomids. The microbiomes of nematodes, chironomids, and bathynellids are composed of members of the Bacteroidetes and Firmicutes phyla, which are related to the symbiotic bacteria found in insects and animals from other ecotopes. Microorganisms typically found in the water and sediments of Lake Baikal were also detected in the invertebrates microbiomes.

A Gram-stain negative, rod shaped, motile by gliding, yellow-pigmented, aerobic bacterium, designated SE-1-eT, was isolated from a soil sample collected on Dokdo Island, South Korea. The isolate was characterized taxonomically using a polyphasic approach based on the phenotypic and genomic analyses. The phylogenetic analysis based on 16S rRNA gene sequence revealed that strain SE-1-eT belonged to the genus Flavobacterium in the family Flavobacteriaceae and had the highest sequence similarity with Flavobacterium cheongpyeongense IMCC34759T (97.5%), Flavobacterium arsenitoxidans S2-3HT (97.4%), Flavobacterium resistens BD-b365T (97.4%), and Flavobacterium chungangense CJ7T (97.4%). The predominant respiratory quinone of the isolate was found to be MK-6; the main polar lipid was phosphatidylethanolamine; and the major fatty acids were identified as summed feature 3 (C16:1 ω7c/C16:1 ω6c), C15:0 iso, and C16:0. The draft genome of strain SE-1-eT had a length of 3,715,609 bp and a DNA G + C content of 34.8 mol%. The nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between the novel isolate and F. cheongpyeongense IMCC34759T, F. resistens BD-b365T, and Flavobacterium chungangense CJ7T ranged from 74.9 to 75.3% and from 20.2 to 20.9%, respectively. On the basis of its phenotypic properties, genotypic distinctiveness, and chemotaxonomic features, strain SE-1-eT represents a novel species in the genus Flavobacterium, for which the name Flavobacterium agrisoli sp. nov. is proposed. The type strain is SE-1-eT (= KCTC 82352 T = JCM 34302 T).

Sediment environments harbor a repertoire of microorganisms that contribute to animal health and the microecosystem in aquaculture ecosystems, but their community diversity and the potential factors that control it remain unclear. Here, we applied 16S rRNA gene amplicon sequencing to investigate bacterial diversity and assembly mechanisms in the sediments of shrimp cultural ponds at the mesoscale. Our results showed that sediment bacterial communities contained 10,333 operational taxonomic units (OTUs) but had only 34 core OTUs and that the relative abundances of these core OTUs were significantly correlated with the physicochemical properties of the sediments. Proteobacteria, Bacteroidetes, Chloroflexi, Cyanobacteria, Acidobacteria, Firmicutes, Actinobacteria, Ignavibacteriae, Spirochaetae and Planctomycetes were the ten most abundant bacterial phyla. Notably, some opportunistic pathogens (e.g. Vibrio and Photobacterium) and potential functional microbes (e.g. Nitrospira, Nitrosomonas, Desulfobulbus and Desulfuromusa) were widely distributed in shrimp cultural pond sediments. More importantly, we found that there was a significant negative but weak distance-decay relationship among bacterial communities in shrimp culture pond sediments at the mesoscale, and that the spatial turnover of these bacterial communities appeared to be largely driven by stochastic processes. Additionally, environmental factors, such as pH and total nitrogen, also played important roles in influencing the sediment bacterial structure. Our findings enhance our understanding of microbial ecology in aquatic ecosystems and facilitate sediment microbiota management in aquaculture. KEY POINTS: • Core bacterial taxa in cultural pond sediments contributed to the shrimp health and element cycling. • There was a significant negative distance-decay relationship among bacterial communities in shrimp culture pond sediments at the mesoscale, and its spatial turnover appeared to be largely driven by stochastic processes. • Environmental factors (e.g. pH and total nitrogen) played important roles in influencing bacterial structure in shrimp cultural pond sediments.

Background Succinate is produced by both human cells and by gut bacteria and couples metabolism to inflammation as an extracellular signaling transducer. Circulating succinate is elevated in patients with obesity and type 2 diabetes and is linked to numerous complications, yet no studies have specifically addressed the contribution of gut microbiota to systemic succinate or explored the consequences of reducing intestinal succinate levels in this setting. Results Using germ-free and microbiota-depleted mouse models, we show that the gut microbiota is a significant source of circulating succinate, which is elevated in obesity. We also show in vivo that therapeutic treatments with selected bacteria diminish the levels of circulating succinate in obese mice. Specifically, we demonstrate that Odoribacter laneus is a promising probiotic based on its ability to deplete succinate and improve glucose tolerance and the inflammatory profile in two independent models of obesity (db/db mice and diet-induced obese mice). Mechanistically, this is partly mediated by the succinate receptor 1. Supporting these preclinical findings, we demonstrate an inverse correlation between plasma and fecal levels of succinate in a cohort of patients with severe obesity. We also show that plasma succinate, which is associated with several components of metabolic syndrome including waist circumference, triglycerides, and uric acid, among others, is a primary determinant of insulin sensitivity evaluated by the euglycemic-hyperinsulinemic clamp. Conclusions Overall, our work uncovers O. laneus as a promising next-generation probiotic to deplete succinate and improve glucose tolerance and obesity-related inflammation.

Phocaeicola vulgatus is one of the most abundant and ubiquitous bacterial species of the human gut microbiota, yet a comprehensive analysis of antibacterial toxin production by members of this species has not been reported. Here, we identify and characterize a previously undescribed antibacterial protein. This toxin, designated BcpT, is encoded on a small mobile plasmid that is largely confined to strains of the closely related species Phocaeicola vulgatus and Phocaeicola dorei. BcpT is unusual in that it requires cleavage at two distinct sites for activation, and we identify bacterial proteases that perform this activation. We further identify BcpT’s receptor as the Lipid A-core glycan, allowing BcpT to target species of other Bacteroidales families. Exposure of cells to BcpT induces a response involving an unusual sigma/anti-sigma factor pair that is likely triggered by cell envelope stress, resulting in the expression of genes that partially protect cells from multiple antimicrobial toxins.

Agricultural productivity of pomegranate can be enhanced by identifying the crop-associated microbial diversity in the rhizosphere region with respect to plant growth promoters and other beneficial organisms. Traditional culture methods have limitations in microbial screening as only 1-2% of these organisms can be cultured. In the present study, 16S rRNA amplicon-based metagenomics approach using MinION Oxford Nanopore platform was employed to explore the microbial diversity in the rhizosphere of pomegranate Bhagwa variety, across variable soil depths from 0 to 5 cms (R2), 5-10 cms (R4) and 10-15 cms (R6), using bulk soil as the control. Across all the three layers, significant variations in pH, nitrogen content and total fungal count were observed. 16S rRNA analysis showed the abundance of planctomycetes, Pirellula staleyi, followed by bacteroidetes, Flavisolibacter LC59 and Niastella koreensis across the various soil depths in the rhizospheric soil samples. Pathway prediction analysis indicated arginine and proline metabolism (gamma-glutamyl putrescine oxidase) and hydrogen sulfide biosynthesis as the most abundant pathway hits. Comparative abundance analysis across layers showed the R6 layer with the maximum microbial diversity in terms of highest dimension of variation (79.2%) followed by R4 and R2 layers (p 0.01). Our analysis shows the significant influence of root zone in shaping microbial diversity. This study has reported the presence of Planctomycetes, Pirellula staleyi for the first time in the pomegranate field.

Sabkhas are hypersaline, mineral-rich, supratidal mudflats that harbor microbes that are adapted to high salt concentration. Sabkha microbial diversity is generally studied for their community composition, but less is known about their genetic structure and heterogeneity. In this study, we analyzed a coastal sabkha for its microbial composition using 16S rDNA and whole metagenome, as well as for its population genetic structure. Our 16S rDNA analysis show high alpha diversity in both inner and edge sabkha than outer sabkha. Beta diversity result showed similar kind of microbial composition between inner and edge sabkha, while outer sabkha samples show different microbial composition. At phylum level, Bacteroidetes (~ 22 to 34%), Euryarchaeota (~ 18 to ~ 30%), unclassified bacteria (~ 24 to ~ 35%), Actinobacteria (~ 0.01 to ~ 11%) and Cyanobacteria (less than 1%) are predominantly found in both inside and edge sabkha regions, whereas Proteobacteria (~ 92 to ~ 97%) and Parcubacteria (~ 1 to ~ 2%) are predominately found in outer sabkha. Our 225 metagenomes assembly from this study showed similar bacterial community profile as observed in 16S rDNA-based analysis. From the assembled genomes, we found important genes that are involved in biogeochemical cycles and secondary metabolite biosynthesis. We observed a dynamic, thriving ecosystem that engages in metabolic activity that shapes biogeochemical structure via carbon fixation, nitrogen, and sulfur cycling. Our results show varying degrees of horizontal gene transfers (HGT) and homologous recombination, which correlates with the observed high diversity for these populations. Moreover, our pairwise population differentiation (Fst) for the abundance of species across the salinity gradient of sabkhas identified genes with strong allelic differentiation, lower diversity and elevated nonsynonymous to synonymous ratio of variants, which suggest selective sweeps for those gene variants. We conclude that the process of HGT, combined with recombination and gene specific selection, constitute the driver of genetic variation in bacterial population along a salinity gradient in the unique sabkha ecosystem.