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Polysaccharides and probiotics can play an outstanding role in the treatment of liver disease by regulating gut microbiota. Recently, the combined therapeutic effect of probiotics and polysaccharides has attracted the attention of researchers. Houttuynia cordata polysaccharide (HCP) combined with Lactiplantibacillus plantarum P101 was used to prevent carbon tetrachloride (CClResults showed that, in mice, HCP combined with L. plantarum P101 significantly alleviated oxidative stress and inflammatory injury in the liver by activating Nrf2 signals and inhibiting NF-κB signals. The analysis of gut microbiota revealed that the combination of HCP and L. plantarum P101 increased the abundance of beneficial bacteria such as Alloprevotella, Roseburia, and Akkermansia, but reduced that of the pro-inflammatory bacteria Alistipes, Enterorhabdus, Anaerotruncus, and Escherichia-Shigella. Correlation analysis also indicated that the expression of Nrf2 and TLR4/NF-κB was connected to the changes in gut microbiota composition. Houttuynia cordata polysaccharide combined with L. plantarum P101 can regulate the gut microbiota and then mediate the gut-liver axis to activate the antioxidant pathway and inhibit inflammatory responses, thereby alleviating CClOur study provided a new perspective on the use of polysaccharides combined with probiotics in the treatment of liver disease. © 2022 Society of Chemical Industry.

A randomized clinical trial with a starch- and sucrose-reduced diet (SSRD) in irritable bowel syndrome (IBS) patients has shown clear improvement of participants' symptoms. The present study aimed to explore the effects of the SSRD on the gut microbiota and circulating micro-RNA in relation to nutrient intake and gastrointestinal symptoms.IBS patients were randomized to a 4-week SSRD intervention (n = 80) or control group (n = 25); habitual diet). At baseline and 4 weeks, blood and fecal samples, 4 day-dietary records, and symptom questionnaires were collected, that is, Rome IV questionnaires, IBS-symptom severity score (IBS-SSS) and visual analog scale for IBS (VAS-IBS). Micro-RNA was analyzed in blood and microbiota in faeces by 16S rRNA from regions V1-V2.The alpha diversity was unaffected, whereas beta diversity was decreased (p 0.001) along with increased abundance of Proteobacteria (p = 0.0036) and decreased abundance of Bacteroidetes phyla (p 0.001) in the intervention group at 4 weeks. Few changes were noted in the controls. The shift in beta diversity and phyla abundance correlated with decreased intakes of carbohydrates, disaccharides, and starch and increased fat and protein intakes. Proteobacteria abundance also correlated positively (RThe SSRD induced a shift in beta diversity along with several bacteria at different levels, associated with changes in nutrient intakes and reduced gastrointestinal symptoms. No corresponding changes were observed in the control group. Neither the nutrient intake nor the microbiota changes affected micro-RNA expression. The study was registered at ClinicalTrials.gov data base (NCT03306381).

Objectives To characterize the abundance and relative composition of seawater bacterioplankton communities in Changle city using Illumina MiSeq sequencing and bacterial culture techniques. Methods Seawater samples and physicochemical factors were collected from the coastal zone of Changle city on 8 September 2019. Nineteen filter membranes were obtained after using a suction filtration system. We randomly selected eight samples for total seawater bacteria (SWDNA group) sequencing and three samples for active seawater bacteria (SWRNA group) sequencing by Illumina MiSeq. The remaining eight samples were used for bacterial culture and identification. Alpha diversity including species coverage (Coverage), species diversity (Shannon–Wiener and Simpson index), richness estimators (Chao1), and abundance‐based richness estimation (ACE) were calculated to assess biodiversity of seawater bacterioplankton. Beta diversity was used to evaluate the differences between samples. The species abundance differences were determined using the Wilcoxon rank‐sum test. Statistical analyses were performed in R environment. Results The Alpha diversity in the SWDNA group in each index was ACE 3206.99, Chao1 2615.12, Shannon 4.64, Simpson 0.05, and coverage 0.97; the corresponding index was ACE 1199.55, Chao1 934.75, Shannon 3.49, Simpson 0.09, and coverage 0.99. The sequencing results of seawater bacterial genes in the coastal waters of Changle city showed that the phyla of high‐abundance bacteria of both the SWDNA and SWRNA groups included Cyanobacteria, Proteobacteria, and Bacteroidetes. The main classes included Oxyphotobacteria, Alphaproteobacteria, and Gammaproteobacteria. The main genera included Synechococcus CC9902, Chloroplast, and Cyanobium_PCC‐6307. Beta diversity analysis showed a significant difference between the SWDNA and SWRNA groups (P, In the SWDNA and SWRNA groups, the dominance of the phyla were Cyanobacteria, Proteobacteria, and Bacteroides; the main classes were oxygen‐producing photobacteria, α‐proteobacteria, and γ‐proteobacteria. The predominant genera are Synechococcus_CC9902, Chloroplast, Cyanobium_PCC‐6307, Candidatus Actinomarina, Ascidiaceihabitans and HIMB11 in SWDNA; Chloroplast, Synechococcus_CC9902, HIMB11, Cyanobium_PCC‐6307, Ascidiaceihabitans, and Ralstonia in SWRNA.

Current studies regarding the effect of different nitrogen sources on gut microbiota have thus far disregarded the ability of probiotics and coliforms to compete for protein. This study aimed to investigate the differences in the utilization of soybean protein (SPro) and its derived peptides (SPep) by the gut microbiota of Sprague Dawley (SD) rats. The SPro and SPep prepared in this study showed extensive SPro molecular weight distribution, while that of SPep was minimal, ranging between 150 and 1000 Da and primarily consisting of two to five amino acids. The cecum microflora composition of the rats was determined via 16S rDNA amplicon sequencing, showing that the SPro and SPep significantly increased the abundance and uniformity of the gut microbiota after 35 days of feeding. The Firmicutes/Bacteroidetes (F/B) ratios of the SPep, SPro, and casein groups were 2.49 ± 0.60, 2.98 ± 1.12, and 2.59 ± 0.74, respectively. Although the rats fed with SPro and SPep displayed similar gut microbiome structures, SPep significantly promoted Lactobacillus and Phascolarctobacterium growth. The results showed that SPep significantly increased the diversity of the gut microbiota and elevated the probiotic proportion. PRACTICAL APPLICATION: SPro and SPep are two nutritious and high-quality nitrogen sources. The results showed that SPro and SPep regulated the structure of gut microbiota in rats, and the effect of SPep was better. This study provides a theoretical basis for developing SPep functional foods able to regulate gut microbiota and maintain health.

BACKGROUND The pathophysiology of the prostate enlargement underlying lower urinary tract symptoms is unknown. Meanwhile, the gut microbiota can contribute to various host conditions. We hypothesized that the gut microbiota plays a role in prostate enlargement. METHODS We included 128 patients who underwent prostate biopsies at our hospitals between December 2018 and March 2020, excluding those who had used antibiotics within the past 6 months and those who were diagnosed with prostate cancer of cT3 or higher. Patients with prostate volumes ≥30 ml were defined as the prostate-enlargement (PE) group; those with prostate volumes

Ectomycorrhiza-associated bacteria, especially endofungal bacterial microbiota (EBM) in the fruiting body, play important roles in driving the establishment and function of ectomycorrhizae. However, the influence of ectomycorrhizal fungus bolete identity on their EBM is still unclear. We analysed the EBM of three different bolete fruiting body species on Thousand Island Lake, including Tylopilus felleus, Tylopilus areolatus and Boletus queletii, and compared them with their corresponding mycosphere soil bacterial microbiota by high-throughput sequencing. The EBM was classified into Bacillus, Pseudomonas, Burkholderia and Stenotrophomonas genera. Proteobacteria, Bacteroidetes and Acidobacteria were predominant in the EBM of bolete fruiting bodies as well as their mycosphere soil, while Firmicutes was significantly higher in the EBM. Moreover, the core microbiome (342 operational taxonomic units) of the EBM was shared among the three bolete fungal species. The relative abundances of gene families related to cell cycle control and nucleotide, coenzyme and lipid metabolism were significantly higher in the EBM than in the corresponding mycosphere soil bacterial microbiota, but there was no difference among the three different boletes. The results suggested that the host identity of ectomycorrhizal fungus boletes could affect the EBM, which might be mainly due to the selection of host fungi for the different functional EBM needed.

Studies on large-sample gut microbial sequencing data indicate that gut microbiota can be divided into multiple community types; different community types may influence the community function and ecosystem service. However, the knowledge on the classification, diversity, interaction, and assembling of microbial community types in the gut of wild animals is still insufficient. Here, we used pika gut microbiota data as an example to study the microbial community types in large-sample sequencing dataset. Cecal microbial communities from 118 wild plateau pika (Ochotona curzoniae) individuals at 5 elevational regions on the Qinghai-Tibet Plateau were analyzed. Our results show that pika gut microbiota can be separated into 2 community types (Cluster I and Cluster II). Cluster I was mainly distributed on the high-elevation regions with more than 3694 m and was most dominated by Firmicutes. Cluster II was from the low-elevation areas (lower than 3580 m), and was predominated by Bacteroidetes. Cluster I had a higher community alpha-diversity and predicted functional diversity than Cluster II, and the beta-diversity and predicted functional profiles of these 2 clusters were significantly different. Network analysis revealed that there were more complex interactions between Cluster I, which had enhanced influence on the co-occurrences of other microbes in the bacterial community when compared to Cluster II. Phylogenetic analysis found that the environmental filtering in the Cluster I was stronger than Cluster II. The assemblages of pika gut bacterial communities were determined mainly by deterministic processes, while the relative importance of deterministic processes accounted for more percentages in the Cluster I than Cluster II. Our results demonstrated that 2 gut microbial community types in pikas had distinct diversity patterns and ecological functions. Current methods are also helpful for identifying gut community types and the related mechanisms behind gut microbiota types in large-sample sequencing data of wild animals.

This study aimed to identify the effects of host species on the gut microbial flora in three species (Hemitragus jemlahicus, Pseudois nayaur, and Ovis orientalis) from the subfamily Caprinae, by excluding the impact of environment factors. We investigated the differences in intestinal flora of three species belonging to Caprinae, which were raised in identical conditions. Fecal samples were collected from tahr, mouflon, and bharal, and the V3–V4 region of the 16S ribosomal RNA gene was analyzed by high‐throughput sequencing. The analysis of 16S rRNA gene sequences reveals that fecal samples were mainly composed of four phyla: Firmicutes, Bacteroidetes, Spirochaetes, and Proteobacteria. The most abundant phyla included Firmicutes and Bacteroidetes accounting for >90% of the bacteria, and a higher Firmicutes/Bacteroidetes ratio was observed in tahrs. Moreover, significant differences existed at multiple levels of classifications in the relative abundance of intestinal flora, differing greatly between species. Phylogenetic analyses based on 16S rRNA gene indicated that mouflon is closely related to bharal, and it is inconsistent with previous reports in the species evolutionary relationships. In this study, we demonstrated that the gut microbiota in tahr had a stronger ability to absorb and store energy from the diet compared with mouflon and bharal, and the characteristics of host–microbiome interactions were not significant., We investigated the differences in intestinal flora of three species belonging to Caprinae living in the same environment and raised in identical conditions. We demonstrated that the microbiota in tahr had a stronger ability to absorb and store energy from the diet compared with mouflon and bharal, and the characteristics of host–microbiome interactions were not significant.

The host‐associated microbiome is an important player in the ecology and evolution of species. Despite growing interest in the medical, veterinary, and conservation communities, there remain numerous questions about the primary factors underlying microbiota, particularly in wildlife. We bridged this knowledge gap by leveraging microbial, genetic, and observational data collected in a wild, pedigreed population of gray wolves (Canis lupus) inhabiting Yellowstone National Park. We characterized body site‐specific microbes across six haired and mucosal body sites (and two fecal samples) using 16S rRNA amplicon sequencing. At the phylum level, we found that the microbiome of gray wolves primarily consists of Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Proteobacteria, consistent with previous studies within Mammalia and Canidae. At the genus level, we documented body site‐specific microbiota with functions relevant to microenvironment and local physiological processes. We additionally employed observational and RAD sequencing data to examine genetic, demographic, and environmental correlates of skin and gut microbiota. We surveyed individuals across several levels of pedigree relationships, generations, and social groups, and found that social environment (i.e., pack) and genetic relatedness were two primary factors associated with microbial community composition to differing degrees between body sites. We additionally reported body condition and coat color as secondary factors underlying gut and skin microbiomes, respectively. We concluded that gray wolf microbiota resemble similar host species, differ between body sites, and are shaped by numerous endogenous and exogenous factors. These results provide baseline information for this long‐term study population and yield important insights into the evolutionary history, ecology, and conservation of wild wolves and their associated microbes.

Bacteroidetes are thought to be specialized for the degradation of algae-derived ocean polysaccharides. Here, we show that Bacteroidetes are the predominant phylum in deep-sea sediments and possess more genes associated with polysaccharides degradation than other bacteria. We have isolated a novel Bacteroidetes species from the deep-sea sediments by using a special polysaccharide containing medium, Maribellus comscasis WC007, which possesses 82 putative polysaccharide utilization loci (PULs) containing 374 glycoside hydrolases and 82 SusC/D pairs (Sus indicates starch utilization system; SusC represents the actual TonB-dependent transporter, and SusD is an associated substrate-binding outer membrane lipoprotein) together with 58 sigma/antisigma factors. Through an in-depth analysis of these PULs, strain WC007 can efficiently degrade numerous different polysaccharides including cellulose, pectin, fucoidan, mannan, xylan and starch, which are verified by growth assays. Notably, we find that cellulose has the most significant growth-promoting effect on M. comscasis WC007. And based on scanning electron microscope observation, transcriptomics and metabolomics, we further report on the underlying mechanisms of cellulose degradation and utilization, as well as potential contributions to the carbon cycle. Overall, our results suggest that Bacteroidetes may play key roles in the carbon cycle, likely due to their high abundance and prominent polysaccharide degradation capabilities.

Climate change is projected to cause increased inflow of terrestrial dissolved organic matter to coastal areas in northerly regions. Estuarine bacterial community will thereby receive larger loads of organic matter and inorganic nutrients available for microbial metabolism. The composition of the bacterial community and its ecological functions may thus be affected. We studied the responses of bacterial community to inflow of terrestrial dissolved organic matter in a subarctic estuary in the northern Baltic Sea, using a 16S rRNA gene metabarcoding approach. Betaproteobacteria dominated during the spring river flush, constituting similar to 60% of the bacterial community. Bacterial diversity increased as the runoff decreased during summer, when Verrucomicrobia, Betaproteobacteria, Bacteroidetes, Gammaproteobacteria and Planctomycetes dominated the community. Network analysis revealed that a larger number of associations between bacterial populations occurred during the summer than in spring. Betaproteobacteria and Bacteroidetes populations appeared to display similar correlations to environmental factors. In spring, freshly discharged organic matter favoured specialists, while in summer a mix of autochthonous and terrestrial organic matter promoted the development of generalists. Our study indicates that increased inflows of terrestrial organic matter-loaded freshwater to coastal areas would promote specialist bacteria, which in turn might enhance the transformation of terrestrial organic matter in estuarine environments.

Background Lactulose was one of the earliest prebiotics to be identified. To assess the potential risk of large intakes of lactulose to the intestinal microbiota, mice were fed a diet containing lactulose (0%, 5% and 15%, w/w) for 2 weeks and the changes in the fecal microbiota were evaluated by 16S rRNA high-throughput sequencing. Results Lactulose intervention decreased the α-diversity of the fecal microbiota in both low-dose and high-dose groups. The relative abundance of Actinobacteria was significantly increased, while that of Bacteroidetes was significantly decreased after lactulose intervention. At the genus level, the relative abundance of Bifidobacterium belonging to Actinobacteria was significantly increased, and that of Alistipes belonging to Bacteroidetes was decreased in both low-dose and high-dose groups. The relative abundance of Blautia was significantly increased from 0.2% to 7.9% in the high-dose group and one strain of Blautia producta was isolated from the mice feces. However, the strain could not utilize lactulose. Conclusion Overall, the microbial diversity was decreased after lactulose treatment, with significant increases in the relative abundance of Bifidobacterium. We also provide a strategy to increase the relative abundance of Blautia in the intestine by lactulose feeding at high doses, although the mechanism is not revealed. This will help us understand the prebiotic effect of lactulose on the host health. © 2021 Society of Chemical Industry.

Aim The β‐diversity of plants and animals generally decreases with increasing latitudes. Here, we tested whether this relationship also holds for soil microbes at both functional and taxonomic levels. Location China. Time period Between June and October 2013. Major taxa studied Soil archaea, bacteria, and functional genes. Methods We used a spatially explicit ‘L‐shaped’ sampling strategy in 39 paddy fields in China to study the pattern of soil microbial β‐diversity (i.e., species turnover, βz) across a latitudinal gradient (19.75° N to 47.58° N), with 11 soil samples taken within a 100 m × 100 m plot from each field. Archaeal and bacterial communities were analysed by sequencing 16S ribosomal RNA gene amplicons using Illumina MiSeq; microbial functional genes involved in C/N/P/S cycling were detected by GeoChip. Results We showed that the microbial β‐diversity varied considerably across taxonomic and functional groups. For both soil microbial communities and functional genes, β‐diversity decreased significantly along elevated latitudes at the continental scale. Woesearchaeota of archaeal communities, Bacteroidetes of bacterial communities, and the functional genes involved in methane production displayed the greatest decreases. Both mean temperature during the growing season of rice plants and paddy soil heterogeneity contributed to the latitudinal patterns. Further analyses indicated that temperature was more important than soil heterogeneity in driving the β‐diversity of microbial communities and functional genes. Main conclusions These results highlight the importance of temperature‐driven soil microbial β‐diversity and suggest the potential to predict the changes of microbial diversity with climate change.

Our study demonstrated that both host species identity and environments combine to shape the composition and function of gut microbiota in the herbivorous mammals. These findings imply that the sympatric herbivorous mammals may relax the interspecific relationship by reshaping the gut microbiota when the food is abundant in summer, and compete for limited food resources by advancing the capacity of gut microbiota in winter., Summary The previous studies have reported that the mammalian gut microbiota is a physiological consequence; nonetheless, the factors influencing its composition and function remain unclear. In this study, to evaluate the contributions of the host and environment to the gut microbiota, we conducted a sequencing analysis of 16S rDNA and shotgun metagenomic DNA from plateau pikas and yaks, two sympatric herbivorous mammals, and further compared the sequences in summer and winter. The results revealed that both pikas and yaks harboured considerably more distinct communities between summer and winter. We detected the over‐representation of Verrucomicrobia and Proteobacteria in pikas, and Archaea and Bacteroidetes in yaks. Firmicutes and Actinobacteria, associated with energy‐efficient acquisition, significantly enriched in winter. The diversity of the microbial community was determined by the interactive effects between the host and season. Metagenomic analysis revealed that methane‐metabolism‐related pathway of yaks was significantly enriched in summer, while some pathogenic pathways were more abundant in pikas. Both pikas and yaks had a higher capacity for lipid degradation in winter. Pika and yak shared more OTUs when food shortage occurred in winter, and this caused a convergence in gut microbial composition and function. From winter to summer, the network module number increased from one to five in pikas, which was different in yaks. Our study demonstrates that the host is a dominant factor in shaping the microbial communities and that seasonality promotes divergence or convergence based on dietary quality across host species identity.

Information on the gut microbiome composition of different mammals could provide novel insights into the evolution of mammals and succession of microbial communities in different hosts. However, there is limited information on the gut microbiome composition of marine mammals, especially cetaceans, because of sampling constraints. In this study, we investigated the diversity and composition of microbial communities in the stomach, midgut, and hindgut of two stranded short-finned pilot whales (Globicephala macrorhynchus) and hindgut of a stranded pygmy sperm whale (Kogia breviceps) by using 16S rRNA gene amplicon sequencing technology. On the basis of the 50 most abundant operational taxonomic units, principal coordinate analysis, and non-metric multidimensional scaling analysis, we confirmed that the gut microbial communities of the three whales were different. Our results revealed that the gut microbiome of one stranded short-finned pilot whale GM16 was dominated by Firmicutes (mainly Clostridium) and Fusobacteria; whereas that of the other pilot whale GM19 was composed of Gammaproteobacteria and Bacteroidetes (mainly Vibrio and Bacteroides, respectively), probably caused by intestinal disease and antibiotic treatment. The gut microbiome of the pygmy sperm whale was dominated by Firmicutes and Bacteroidetes. Moreover, different gastrointestinal tract regions harbored different microbial community structures. To our knowledge, this is the first report of the gut microbiome of short-finned pilot whales, and our findings will expand our current knowledge on microbial diversity and composition in the gastrointestinal tract of cetaceans. This article is protected by copyright. All rights reserved.

Porphyromonas gingivalis is a Gram-negative anaerobic pathogen found in subgingival plaque associated with progressive periodontitis. Proteins associated with the outer membrane (OM) of Gram-negative pathogens are particularly important for understanding virulence and for developing vaccines. The aim of this study was to establish a reliable list of outer membrane associated proteins (Omps) for this organism. Starting with a list of 99 experimentally determined Omps, several bioinformatics tools were used to predict a further 52 proteins, leading to a predicted OM proteome of 151 proteins. The tools used included databases of protein families, prediction of OM β-barrels and structural homology. The list includes 33 T9SS cargo proteins, 43 lipoproteins and 66 OM β-barrel proteins with some overlap between categories. The proteins are discussed both in these structural categories as well as their various functions in OM biogenesis, nutrient acquisition, protein secretion, adhesion and efflux. Proteins that were previously shown to be part of large complexes are highlighted and cross reference is provided to a previous major study of protein localization in P. gingivalis. Finally, proteins were also scored according to their level of conservation within the Bacteroidales taxon. Low scores were shown to correlate with virulence factors and may be predictive of novel virulence factors.

As predators of bacteria, amoebae select for traits that allow bacteria to become symbionts by surviving phagocytosis and exploiting the eukaryotic intracellular environment. Soil-dwelling social amoebae can help us answer questions about the natural ecology of these amoeba-bacteria symbioses along the pathogen-mutualist spectrum. Our objective was to characterize the natural bacterial microbiome of phylogenetically and morphologically diverse social amoeba species using next-generation sequencing of 16S rRNA amplicons directly from amoeba fruiting bodies. We found six phyla of amoeba-associated bacteria: Proteobacteria, Bacteroidetes, Actinobacteria, Chlamydiae, Firmicutes, and Acidobacteria. The most common associates of amoebae were classified to order Chlamydiales and genus Burkholderia-Caballeronia-Paraburkholderia. These bacteria were present in multiple amoeba species across multiple locations. While there was substantial intraspecific variation, there was some evidence for host specificity and differentially abundant taxa between different amoeba hosts. Amoebae microbiomes were distinct from the microbiomes of their soil habitat, and soil pH affected amoeba microbiome diversity. Alpha-diversity was unsurprisingly lower in amoebae samples compared with soil, but beta-diversity between amoebae samples was higher than between soil samples. Further exploration of social amoebae microbiomes may help us understand the roles of bacteria, host, and environment on symbiotic interactions and microbiome formation in basal eukaryotic organisms.

Background The human and domestic animal faecal microbiota can carry various antimicrobial resistance genes (ARGs), especially if they have been exposed to antimicrobials. However, little is known about the ARG profile of the faecal microbiota of healthy foals. A high-throughput qPCR array was used to detect ARGs in the faecal microbiota of healthy foals. Objectives To characterise the faecal microbiota and ARG profiles in healthy Australian foals aged less than 1 month. Study design Observational study. Methods The faecal microbiota and ARG profiles of 37 Thoroughbred foals with no known gastrointestinal disease or antimicrobial treatment were determined using 16S rRNA gene sequencing and a high-throughput ARG qPCR array. Each foal was sampled on one occasion. Results Firmicutes and Bacteroidetes were dominant in the faecal microbiota. Foals aged 1-2 weeks had significantly lower microbiota richness than older foals. Tetracycline resistance genes were the most common ARGs in the majority of foals, regardless of age. ARGs of high clinical concern were rarely detected in the faeces. The presence of ARGs was associated with the presence of class I integron genes. Main limitations Samples were collected for a case-control study so foals were not sampled longitudinally, and thus the development of the microbiota as individual foals aged could not be proven. The history of antimicrobial treatment of the dams was not collected and may have affected the microbiota of the foals. Conclusion The ARGs in foal faeces varied concomitantly with age-related microbiota shifts. The high abundance of tetracycline resistance genes was likely due to the dominance of Bacteroides spp.

Aims/Introduction Gut dysbiosis is generally associated with type 2 diabetes mellitus. However, the effect of habitual dietary intake on gut dysbiosis in Japanese patients with type 2 diabetes mellitus has not yet been explicated. This study investigated whether alteration of the gut microbiota was influenced by dietary intake of sucrose in Japanese patients with type 2 diabetes mellitus. Materials and Methods In this cross‐sectional study, 97 patients with type 2 diabetes mellitus and 97 healthy individuals were matched by age and sex, and then, fecal samples were obtained. Next‐generation sequencing of the 16S ribosomal ribonucleic acid gene was carried out, and functional profiles for the gut microbiota were analyzed. We selected the top 30 gut microbial genera and top 20 functional profiles for the gut microbiota specified by the weighted average difference method. The association between gut microbial genera or functional profiles and habitual dietary intake was investigated by Spearman’s rank correlation coefficient, and then, clustering analysis was carried out to clarify the impact of habitual dietary intake. Results The Actinobacteria phylum was highly abundant in patients with type 2 diabetes mellitus, whereas the Bacteroidetes phylum was less abundant. Diabetic‐type gut microbes, specifically Bacteroides and Bifidobacterium, were altered by sucrose intake at the genus level. Furthermore, sucrose intake was associated with glycolysis/gluconeogenesis in the diabetic‐type functional profiles of the gut microbiota. Conclusions The gut microbiota and functional profiles for the gut microbiota in patients with type 2 diabetes mellitus were significantly different from those in healthy individuals. Furthermore, we showed that sucrose intake was closely associated with these differences., Gut dysbiosis and change of functional profiles of the gut microbiota exist in Japanese patients with type 2 diabetes mellitus. Diet habit, especially sucrose intake, has a close association with these changes.

Dogs and cats have gained a special position in human society by becoming our principal companion animals. In this context, efforts to ensure their health and well‐fare have increased exponentially, with in recent times a growing interest in assessing the impact of the gut microbiota on canine and feline health. Recent technological advances have generated new tools to not only examine the intestinal microbial composition of dogs and cats, but also to scrutinize the genetic repertoire and associated metabolic functions of this microbial community, revealing that the taxonomic composition and the metabolic repertoire of the intestinal microbial population of dogs and cats may be influenced by several factors, including diet, age and anthropogenic aspects, as well as intestinal dysbiosis., Summary Dogs and cats have gained a special position in human society by becoming our principal companion animals. In this context, efforts to ensure their health and welfare have increased exponentially, with in recent times a growing interest in assessing the impact of the gut microbiota on canine and feline health. Recent technological advances have generated new tools to not only examine the intestinal microbial composition of dogs and cats, but also to scrutinize the genetic repertoire and associated metabolic functions of this microbial community. The application of high‐throughput sequencing techniques to canine and feline faecal samples revealed similarities in their bacterial composition, with Fusobacteria, Firmicutes and Bacteroidetes as the most prevalent and abundant phyla, followed by Proteobacteria and Actinobacteria. Although key bacterial members were consistently present in their gut microbiota, the taxonomic composition and the metabolic repertoire of the intestinal microbial population may be influenced by several factors, including diet, age and anthropogenic aspects, as well as intestinal dysbiosis. The current review aims to provide a comprehensive overview of the multitude of factors which play a role in the modulation of the canine and feline gut microbiota and that of their human owners with whom they share the same environment.

The objective of this study was to investigate the characteristics of ruminal microbial communities of alpacas (Lama pacos) and sheep (Ovis aries) fed three diets with varying ratios of roughage (corn stalk) to concentrate, 3:7 (LS), 5:5 (MS) and 7:3 (HS). Six alpacas (one-year-old and weighing 29.5 ± 7.1 kg) and six sheep (one-year-old and weighing 27.9 ± 2.7 kg) were used in this study, in a replicated 3 × 3 Latin square experiment. Total protozoa concentration was determined under the microscope; total fungi and methanogens were assessed using quantitative polymerase chain reaction and expressed as a percentage of total bacterial 16S rRNA gene copies; bacterial communities were investigated by targeted 16S rRNA gene (V3-V4 region) sequencing. The percentage of fungi was significantly higher in alpacas than in sheep under the LS diet, while the concentration of protozoa was significantly lower in alpacas under HS, MS and LS diets. The alpha diversity including Shannon, Chao l and ACE indices of bacterial communities was higher in alpacas than in sheep, under the LS diet. A total of 299 genera belonging to 22 phyla were observed in the forestomach of alpaca and sheep, with Bacteroidetes and Firmicutes dominating both animal species. Phyla Armatimonadetes and Fusobacteria, as well as 64 genera, were detected only in alpacas, whereas phyla Acidobacteria and Nitrospira, as well as 44 genera, were found only in sheep. The abundance of cellulolytic bacteria, including Butyrivibrio and Pseudobutyrivibrio, was higher in alpacas than in sheep under all three diets. These differences in the forestomach microbial communities partly explained why alpacas displayed a higher poor-quality roughage digestibility, and a lower methane production. Results also revealed that the adverse effects of high-concentrate diets (70%) were lesser in alpacas than in sheep.

AIM To identify dominant microorganisms in root filled teeth with apical periodontitis by Pan-PCRs in comparison with a culture-dependent approach, focusing on fungal species profiling. METHODOLOGY The root filling material (gutta-percha) removed from 42 teeth with periapical radiolucencies undergoing root canal retreatments was analysed by molecular genetics techniques. Real-Time Pan-PCRs were conducted for the diagnosis of predominant bacteria (targeting 16S rDNA) and fungi (targeting ITS1-2 region). Identification of microorganisms was performed by Sanger sequencing of the PCR products and BLAST analysis. Additionally, subgingival plaque samples were collected and cultured to review the composition of the microbial flora. The McNemar test and the repeated measures anova were used for statistical analyses (significance level was set at P

Background and aim Human gut microbiota play an important role in metabolism and host physiology. Perturbations of the gut microbial communities lead to the development of various diseases such as inflammatory bowel disease, celiac disease, allergic diseases, and metabolic diseases. Crohn's disease is a chronic inflammatory bowel disease characterized by periods of remission and relapse. Several studies suggest that intestinal inflammation arises due to an abnormal response of the intestinal immune system to the fecal microbiota. The goal of the study was to evaluate the relative amount of four bacterial groups in fecal samples of Crohn's disease patients and their relation to the inflammatory activity. Methods We studied stool samples of 105 individuals, 54 with Crohn's disease and 51 as a control group. The DNA extracted from the stool samples was subjected to real‐time polymerase chain reaction (qPCR) for quantification of the Bacteroidetes phylum, class Bacilli, and Bifidobacteriaceae and Enterobacteriaceae families. Results We found a significant increase in Bacteroidetes in Crohn's disease samples when compared to the control group (14 650 and 2060 CFU/ng DNA, respectively) (P = 0.014). On the other hand, we observed a significant reduction in Bacilli and Bifidobacteriaceae (13 and 58 CFU/ng DNA, respectively) (P, Gut microbiota is strongly associated with host physiology, and perturbations of the gut microbial communities lead to the development of various diseases. The goal of this study was to evaluate the relative amount of four bacterial groups in fecal samples of patients with Crohn's disease and their relation to the inflammatory activity. We observed that the commensal bacteria were decreased in fecal samples of participants with Crohn´s disease when compared to the control group. There was no relation between the disease localization and/or clinical condition with the microbiota.

AIM To assess in a cross-sectional clinical study the effect of antibiotics on the diversity, structure and metabolic pathways of bacterial communities in various oral environments in patients with acute primary infections. METHODOLOGY Samples of saliva (SA), supragingival biofilm (SB) and from the pulp cavity (PC) were collected from teeth with acute primary infections and then grouped according to previous use of antibiotics (NoAtb = no antibiotics [n = 6]; Atb = antibiotics [n = 6]). DNA sequencing was conducted using MiSeq (Illumina, San Diego, CA, USA). The V1-V3 hyper-variable region of the 16S rRNA gene was amplified. A custom Mothur pipeline was used for 16S rRNA processing. Subsequent analyses of the sequence dataset were performed in R (using vegan, phyloseq and ggplot2 packages) or QIIME. RESULTS Twelve patients aged from 22 to 56 years were recruited. Participants in the Atb group had taken the beta-lactamics amoxicillin (5/6) or cephalexin (1/6) for 2-3 days. A total of 332 bacterial taxa (OTUs) were identified, belonging to 120 genera, 60 families and nine phyla. Firmicutes (41%) and Bacteroidetes (38%) were the most abundant phyla in all samples. Taxa clustered significantly by oral site (PCoA analysis; P

Parkinson's disease is a common degenerative disease of the elderly. Although the majority of studies have focused on the central nervous system (CNS) features of Parkinson's disease, recent findings suggest there is a functional link between the gut microbiome and the hallmarks of the disease. PubMed, Web of Science, EMBASE and other Chinese and English databases were searched for relevant literature. Studies on changes to intestinal microbiota in Parkinson's patients were retrieved and systematically reviewed. Quality filtering, clustering and species annotation were performed on 16s sequencing raw data from retrieved studies to achieve comparability across studies. Alpha-diversity indices and a random effect model were used to analyse significantly altered microbiota. A total of nine studies were included in this retrospective analysis, four of which contained raw data. Alpha diversity was significantly different between control and Parkinson's disease patients in two of the four studies. Using the raw data from four individual studies, we observed differences in the phlya Bacteroidetes and Actinobacteria. Additionally, differences were observed between control and Parkinson's disease patients at the level of family (Prevotellacaea and Lactobacillaceae) and genus (Bifidobacterium and Clostridium). This study confirmed that changes in the microbiome are a consistent feature of Parkinson's disease patients and, therefore, may contribute to the onset of disease.

Objective To assess the bacterial characteristics associated with intra-oral halitosis among Chinese preschool children. Methods An epidemiological study was conducted among 273 preschool children (aged 3-4 years) in Shanghai, China, followed by the collection of 16 samples from the tongue coating of caries-free healthy and halitosis participants. The characterization of associated microbial communities was performed using 16S rRNA gene sequencing on the MiSeq. Results Halitosis was observed in 13.2% of the preschool children. No significant difference in terms of microbial diversity (p > .05) was detected in the control and halitosis groups. The dominant bacterial genera observed in both groups included Prevotella, Veillonella, Streptococcus, Neisseria, Actinomyces, Haemophilus, and Leptotrichia. The relative proportions of thirteen species (including Leptotrichia sp. HMT_417, Prevotella Pallens, and Alloprevotella rava) were significantly higher in the halitosis group compared with the control group, whereas the distribution of seventeen species from genera Streptococcus, Gemella, and Kingella showed a higher abundance in the control group. Further investigation of interactions among species demonstrated obvious differences in two groups, indicating that various microorganisms interact to produce halitosis in preschool children. Conclusions Overall, halitosis is associated with multi-microbial mutual interactions. The oral flora microorganisms may exert potentiating or inhibiting effects on each other.

Although soil microbial communities are central in ecosystem functioning, we know little of their characterization for those associated with grazing‐tolerant host plant species in grassland ecosystems in response to grazing. In this study, we used a high‐throughput sequencing approach to characterize soil microbes from the rhizosphere and bulk soil of grazing‐tolerant grass species, Stipa breviflora, in the Inner Mongolian desert steppe. We found that response mechanisms of soil bacteria distinct from fungal communities, and variance also occur between the rhizosphere and bulk soil communities under long‐term grazing. Soil fungal communities and the co‐occurrence networks in S. breviflora rhizosphere were more sensitive to long‐term grazing than bacteria. We reveal that rhizosphere effects and soil water content were the main drivers of the changes in fungal communities and their co‐occurrence networks. Moreover, the dominant bacterial phyla Bacteroidetes and Proteobacteria and fungal phyla Ascomycota and Glomeromycota might participate in regulating processes of S. breviflora's response to grazing. Overall, these findings give new snapshots of mechanisms of how grazing affects soil microbial communities, in an attempt to contribute to a clearer understanding of grazing‐tolerant mechanism of S. breviflora., In this study, we used a random matrix theory (RMT)‐based network approach to investigate the characterization of soil microbes associated with a grazing‐tolerant grass species, Stipa breviflora. I believe the results would provide new insight into the mechanisms by which grazing affects soil microbial communities, so as to contribute to a better understanding of grazing‐tolerant mechanism of S. breviflora.

The mammalian intestinal microbiome is critical for host health and disease resistance. However, the cetacean intestinal microbiota remains relatively unexplored. By using high-throughput 16S rRNA gene sequencing, we analyzed intestinal bacterial samples from an Indo-pacific humpback dolphin (Sousa chinensis) stranded near the Pearl River Estuary in China. The samples included 3 anatomical regions (foregut, midgut, and rectum) and 2 anatomical locations (content and mucus). Our analyses revealed that the dolphin intestinal bacteria contained 139 operational taxonomic units (OTUs), dominated at the phyla level by Firmicutes (47.05% in the content; 94.77% in the mucus), followed by Bacteroidetes (23.63% in the content; 1.58% in the mucus) and Gammaproteobacteria (14.82% in the content; 2.05% in the mucus). The intestinal bacteria had a small core community (15 OTUs, accounting for 99.74% of the reads), some of which could be potentially pathogenic to both human and dolphins. As an alternative to sampling the dolphin intestinal bacteria, fecal sampling could be used. Additionally, function potentials such as, xenobiotics biodegradation, beta-lactam resistance, and human disease-related pathways, were detected in the dolphin intestinal bacteria. These findings provide the first baseline knowledge of the intestinal microbiome of the Indo-Pacific humpback dolphin, which may offer new insights into cetacean conservation by using microbial surveillance.

Cardinium and Wolbachia are maternally inherited bacterial symbionts of arthropods that can manipulate host reproduction by increasing the fitness of infected females. Here, we report that Cardinium and Wolbachia coinfection induced male-killing and cytoplasmic incompatibility (CI) when they coexisted in a cryptic species of whitefly, Bemisia tabaci Asia II7. Cardinium and Wolbachia symbionts were either singly or simultaneously localized in the bacteriocytes placed in the abdomen of B. tabaci nymphs and adults. Cardinium-Wolbachia coinfection induced male-killing and resulted in a higher female sex ratio in the intraspecific amphigenetic progeny of Asia II7 ICWH and ICWL lines; interestingly, male-killing induction was enhanced with increased Cardinium titer. Moreover, single infection of Wolbachia induced partial CI in the Asia II7 IW line and resulted in reduced fecundity, higher embryonic mortality, and lower female sex ratio. The uninfected Asia II7 IU line had significantly higher fecundity, lower embryonic and nymphal mortalities, and a lower level of CI than both the Wolbachia-infected Asia II7 IW line and the Cardinium-Wolbachia-coinfected Asia II7 ICWH line. Our findings indicate that Cardinium-Wolbachia coinfection induced male-killing, which may have had antagonistic effects on Wolbachia-induced CI in the Asia II7 whiteflies. For the first time, our study revealed that B. tabaci Asia II7 reproduction is co-manipulated by Cardinium and Wolbachia endosymbionts.

A 2 × 3 factorial design experiment was conducted to examine the effects of reducing dietary crude protein (CP) concentration and/or supplementation with zinc oxide (ZnO) or laminarin on faecal scores (FS) and the large intestinal microbiota post-weaning (PW). One hundred and forty-four pigs were assigned to (T1) 21% standard CP diet (SCP); (T2) SCP + ZnO (SCP ZnO); (T3) SCP + laminarin (SCP LAM); (T4) 18% low CP diet (LCP); (T5) LCP + ZnO (LCP ZnO); and (T6) LCP + laminarin (LCP LAM; n = 8 replicates/treatment). The LCP diet had no effect on FS (p > .05), it increased two measures of alpha diversity, reduced Bacteroidetes and increased Enterobacteriaceae and Helicobacteraceae in the colon relative to the SCP diet (p < .05). ZnO supplementation reduced FS and increased Ruminococcaceae compared with unsupplemented pigs (p < .05). ZnO supplementation increased the genera Frisingicoccus (p < .001), Lachnoclostridium (p < .05) and Peptoclostridium (p < .05) in the colon and reduced total caecal volatile fatty acids (VFA) concentrations compared with the unsupplemented and laminarin-supplemented pigs. Laminarin supplementation reduced FS compared with unsupplemented pigs but had no major effect on the microbiota compared with the unsupplemented pigs. There were CP concentration × additive interactions on both Firmicutes and Proteobacteria. Firmicutes were increased in the LCP ZnO group compared with the LCP group, but there was no difference between the SCP groups. Proteobacteria were reduced in the LCP ZnO group compared with the LCP and LCP LAM groups (p < .05), but there was no difference between the SCP groups. In conclusion, reducing CP did not improve FS; it increased the relative abundance of Enterobacteriaceae; however, it also increased bacterial diversity. Supplementation with ZnO and laminarin improved FS, although all groups had scores within the healthy range. ZnO altered the large intestinal microbiota and VFA concentrations; however, laminarin did not enhance these parameters, suggesting these compounds have differing modes of action.

Background and Aim: Recent researches have shown an altered gut microbiota in celiac disease (CD) patients compared with healthy controls (HCs). This study aims to evaluate the composition of the microbiota of CD children at onset and the relationship between bacterial abundances and symptoms. Methods: Celiac disease patients were consecutively enrolled at a pediatric unit referring for suspected CD. HCs were also included in the study. Stool and duodenal samples were collected and evaluated by a high taxonomic fingerprint microbiota array. Results: Thirty-seven subjects enrolled: 21 CD patients and 16 HCs. Fourteen subjects were male (38%). The mean age was 75months (standard deviation 31.5) for CD patients and 71months (standard deviation 34.9) for HCs. Duodenal microbiota of CD patients showed a dominance of Enterobacteriaceae and subdominance of Bacteroidetes/Streptococcus. Stool microbiota showed a lower abundance of Bacteroides–Prevotella (P=0.013), Akkermansia (P=0.002), and Staphylococcaceae (P=0.001) in CD patients compared with HC. At symptoms level, an increased mean relative abundance of Bacillaceae and Enterobaeriaceae in patients with abdominal pain (P=0.007 and P=0.010) was found. CD patients with diarrhea had reduced mean relative abundance of Clostridium cluster XIVa (P=0.044) and Akkermansia (P=0.033) and an increase in Bacillaceae (P=0.048) and Fusobacterium (P=0.048). Conclusions: Gut microbiota of CD children at disease onset is different from that of HC. Pro-inflammatory microbiota imbalances were associated with CD symptoms. Further studies are needed to assess whether dysbiosis is associated with CD early onset and symptoms.

Despite the widespread distribution of proteorhodopsin (PR)-containing bacteria in the oceans, the use of light-derived energy to promote bacterial growth has only been shown in a few bacterial isolates, and there is a paucity of data describing the metabolic effects of light on environmental photoheterotrophic taxa. Here, we assessed the effects of light on the taxonomic composition, cell integrity and growth responses of microbial communities in monthly incubations between spring and autumn under different environmental conditions. The photoheterotrophs expressing PR in situ were dominated by Pelagibacterales and SAR116 in July and November, while members of Euryarchaeota, Gammaproteobacteria and Bacteroidetes dominated the PR expression in spring. Cell-membrane integrity decreased under dark conditions throughout most of the assessment, with maximal effects in summer, under low-nutrient conditions. A positive effect of light on growth was observed in one incubation (out of nine), coinciding with a declining phytoplankton bloom. Light-enhanced growth was found in Gammaproteobacteria (Alteromonadales) and Bacteroidetes (Polaribacter and Tenacibaculum). Unexpectedly, some Pelagibacterales also exhibited higher growth rates under light conditions. We propose that the energy harvested by PRs helps to maintain cell viability in dominant coastal photoheterotrophic oligotrophs while promoting the growth of some widespread taxa benefiting from the decline of phytoplankton blooms.

Obesity and related metabolic disorders are associated with intestinal microbiota dysbiosis, disrupted intestinal barrier, and chronic inflammation. Neohesperidin (Neo), a natural polyphenol abundant in citrus fruits, is known for its preventative and therapeutic effects on numerous diseases. Here, we report that Neo administration attenuates weight gain, low-grade inflammation, and insulin resistance in mice fed high-fat diet (HFD). Also, Neo administration substantially restores gut barrier damage, metabolic endotoxemia, and systemic inflammation. Sequencing of 16S rRNA genes in fecal samples revealed that Neo administration reverses HFD-induced intestinal microbiota dysbiosis: an increase in the diversity of gut microbiota and alteration in the composition of intestinal microbiota (particularly in the relative abundances of Bacteroidetes and Firmicutes). Furthermore, systemic antibiotic treatment abolishes the beneficial effects of Neo in body weight control, suggesting that the effect of Neo on obesity attenuation largely depends on the gut microbiota. More importantly, we demonstrate that the impact of Neo on the regulation of obesity could be transferred from Neo-treated mice to HFD-fed mice via fecal microbiota transplantation. Collectively, our data highlight the efficacy of Neo as a prebiotic agent for attenuating obesity, implying a potential mechanism for gut microbiota mediated the beneficial effect of Neo.

Background and Aim: Altered gut microbiota have been suggested as part of an etiology of irritable bowel syndrome (IBS), but studies have shown contrasting results. Our aim was to examine gut microbiota composition in a large population-based cohort, with respect to presence and severity of bowel symptoms. Methods: The study cohort consisted of 1988 participants of the Malmo Offspring Study (mean age 40 years, 53% women). From a questionnaire, 19% reported having bowel symptoms the last 2 weeks and 15% reported having IBS. Bowel symptoms were assessed by a validated set of questions with visual analog scales. Gut microbiota was assessed by 16S rRNA gene sequencing (300 bp*2 in V1–V3 region) from fecal samples. The association between abundance of bacteria at genus level and bowel symptoms was calculated by logistic regression or general linear model, adjusted for false discovery rate (q

Interactions between gut microbiota not only regulate physical health, but also form a vital bridge between the environment and the host, thus helping the host to better adapt to the environment. The improvement of modern molecular sequencing techniques enables in‐depth investigations of the gut microbiota of vertebrate herbivores without harming them. By sequencing the 16S rRNA V4‐V5 region of the gut microbiota of both the captive and wild kiang in winter and summer, the diversity and function of the microbiota could be compared. The reasons for observed differences were discussed. The results showed that the dominant phyla of the kiang were Bacteroidetes and Firmicutes, and the structure and abundance of the gut microbiota differed significantly between seasons and environments. However, the relatively stable function of the gut microbiota supplies the host with increased adaptability to the environment. The diversity of the intestinal flora of the kiang is relatively low in captivity, which increases their risk to catch diseases to some extent. Therefore, importance should be attached to the impact of captivity on wildlife., The alpha diversity of gut microbiomes in the wild group was significantly higher than that in the captive group. The content of pathogenic bacteria increased in the captive group. The health level of the captive kiang was lower than that of the wild kiang.

Summary The potential utility of black soldier fly larvae (BSFL) to convert animal waste into harvested protein or lipid sources for feeding animal or producing biodiesel provides a new strategy for agricultural waste management. In this study, the taxonomic structure and potential metabolic and nutrient functions of the intestinal bacterial communities of BSFL were investigated in chicken and swine manure conversion systems. Proteobacteria, Firmicutes and Bacteroidetes were the dominant phyla in the BSFL gut in both the swine and chicken manure systems. After the larvae were fed manure, the proportion of Proteobacteria in their gut significantly decreased, while that of Bacteroidetes remarkably increased. Compared with the original intestinal bacterial community, approximately 90 and 109 new genera were observed in the BSFL gut during chicken and swine manure conversion, and at least half of the initial intestinal genera found remained in the gut during manure conversion. This result may be due to the presence of specialized crypts or paunches that promote microbial persistence and bacteria–host interactions. Ten core genera were found in all 21 samples, and the top three phyla among all of the communities in terms of relative abundance were Proteobacteria, Firmicutes and Bacteroidetes. The nutrient elements (OM, TN, TP, TK and CF) of manure may partly affect the succession of gut bacterial communities with one another, while TN and CF are strongly positively correlated with the relative abundance of Providencia. Some bacterial taxa with the reported ability to synthesize amino acids, Rhizobiales, Burkholderia, Bacteroidales, etc., were also observed in the BSFL gut. Functional analysis based on genes showed that intestinal microbes potentially contribute to the nutrition of BSFL and the high‐level amino acid metabolism may partly explain the biological mechanisms of protein accumulation in the BSFL body. These results are helpful in understanding the biological mechanisms of high‐efficiency nutrient conversion in BSFL associated with intestinal microbes., The potential utility of black soldier fly larvae (BSFL) to convert animal waste into harvested protein or lipid sources provides a new strategy for agricultural waste management. In this study, the taxonomic structure and potential metabolic and nutrient functions of the intestinal bacterial communities of BSFL were investigated in chicken and swine manure conversion systems. The results are helpful in understanding the biological mechanisms of high‐efficiency nutrient conversion in BSFL associated with intestinal microbes.

The gut microbiota of birds is known to be characterized for different species, although it may change with feeding items. In this study, we compared the gut microbiota of birds with different feeding behaviors in the same habitat. We collected fecal samples from three Arctic species, snow buntings Plectrophenax nivalis, sanderlings Calidris alba, and pink‐footed geese Anser brachyrhynchus that are phylogenetically quite distant in different families to evaluate effects of diet on gut microbiota. Also, we characterized the prevalence of fecal bacteria using the Illumina MiSeq platform to sequence bacterial 16S rRNA genes. Our NMDS results showed that fecal bacteria of snow buntings and sanderlings were significantly distant from those of pink‐footed geese. Although all three birds were occupied by three bacterial phyla, Proteobacteria, Firmicutes, and Bacteroidetes, dominant taxa still varied among the species. Our bacterial sequences showed that snow buntings and sanderlings were dominated by Firmicutes and Bacteroidetes, while pink‐footed geese were dominated by Proteobacteria. In addition, the bacterial diversity in snow buntings and sanderlings was significantly higher than that in pink‐footed geese. Our results suggest that insectivorous feeding diet of snow buntings and sanderlings could be responsible for the similar bacterial communities between the two species despite the distant phylogenetic relationship. The distinctive bacterial community in pink‐footed geese was discussed to be related with their herbivorous diet., We showed that fecal bacteria of snow buntings and sanderlings were distant from those of pink‐footed geese. In addition, the bacterial diversity in snow buntings and sanderlings was significantly higher than that in geese. Our results suggest that diet as well as host phylogeny may affect the gut microbiota of Arctic birds.

Despite the vast carbon (C) stock of crop root residues in arable ecosystems, the microbial assimilation mechanism of crop root derived‐C is poorly understood. In this study, a DNA‐based stable isotope probing (DNA‐SIP) approach was used to explore and characterize the diversity of the soil bacterial community assimilating C derived from ¹³C‐labelled rice root residues during a 90‐day incubation. Overall, ¹³C‐assimilating bacterial groups with various characteristics were identified with the occurrence of strong priming effects on soil native C. Significant increases of Actinobacteria, Proteobacteria and Bacteroidetes abundances within the ¹³C‐assimilating bacterial community were observed. Generally, Streptomyces were the predominant utilizers of ¹³C derived from rice root residues within a 28‐day incubation. The ¹³C‐labelling of Pseudomonas, which was continuously detected during incubation, indicated stronger effects at the later decomposition stage. The role of genera Kitasatospora, Catenulispora, Nocardioides, Flavisolibacter and Niastella in ¹³C‐labelled rice root residues assimilation was also observed. Meanwhile, incorporation of rice root residues stimulated the growth of certain bacterial groups that incorporated unlabelled native soil C, including Chloroflexi, Acidobacteria, Planctomycetes, Verrumicrobia and Nitrospirae. HIGHLIGHTS: The microbial mechanism of the utilization of crop root residues is largely neglected. We explored the diversity of bacterial communities assimilating rice root residues with DNA‐SIP Actinobacteria, Proteobacteria and Bacteroidetes were dominant decomposers of root residues Streptomyces and Pseudomonas were consistently detected as key assimilators during decomposition

Background: The role of gut microbiota in metabolic diseases has recently been widely verified. Thyroid hormones are essential for the regulation of energy homeostasis and metabolic processes. However, the relationship between thyroid function and host gut microbial communities is not properly understood. Method: To determine whether and how gut microbiota is associated with thyroid function, metagenomics analysis of the bacterial population in fecal samples of rat models of hyperthyroidism (induced by levothyroxine) and hypothyroidism (induced by propylthiouracil or thyroidectomy) was conducted through 16SrRNA gene sequencing. Finding: Our results revealed that all thyroid dysfunction models were definitely established and gut microbial composition varied according to different thyroid functional status. The relative abundance of Ruminococcus was significantly higher in the hyperthyroidism group (HE) vs both the normal and hypothyroidism (HO) groups while S24-7 was significantly higher in the HO group compared to both the normal and HE groups. The relative abundance of Prevotellaceae and Prevotella were significantly lower in the HO group vs the normal. Firmicutes and Oscillospira was significantly higher in the SHO (surgery-induced hypothyroidism) group than the SHAM group, while Prevotellaceae andPrevotella showed lower abundance in the SHO group compared to the SHAM group. Interpretation: This is the first perspective study of the relationship between thyroid gland and gut microbiota using Next Generation Sequencing-based microbial identification technology. We demonstrated that thyroid status and function influenced the gut microbial composition, and the results presented here can be used as reference in future studies to identify potential mechanism(s) by which thyroid modulates gut microbial population. Funding Statement: This work was supported by a National Research Foundation (NRF) of Korea Grant funded by the Korean Government (NRF- 2019R1A2B5B01070365). This work was also supported by the Main Research Program (E0170602-02) of the Korea Food Research Institute (KFRI) funded by the Ministry of Science and ICT. Declaration of Interests: The authors declare no conflict of interest. Ethics Approval Statement: The animal experimental protocol was approved by the Institutional Animal Care and Use Committee of Dongguk University (approval no. 2015-08128) and all experiments were conducted in accordance with the Guide for the Care and Use of Laboratory Animals

Background Many immune checkpoint inhibitors (ICIs) have been approved in China to treat non‐small cell lung cancer (NSCLC). However, in the long term, less than 20% of patients benefit from ICIs. To maximize the benefit for NSCLC patients, it is necessary to guide the choice of immunotherapy through biomarkers. Recent studies have shown that gut microbiota can affect tumor response to immunotherapy and might be a potential predictive biomarker. This study analyzed the relationship between intestinal flora structure and metabolomic characteristics in NSCLC and the efficacy of ICIs. Methods Prospective analysis of samples from 63 patients with advanced NSCLC who attended the Department of Respiratory Medicine of the Peking Union Medical College Hospital from March 2018 to June 2019, and were prescribed programmed cell death 1 (PD‐1) inhibitors, was carried out. The follow‐up deadline was 31 December 2019. Stool samples were collected from all patients before the start of immunotherapy. DNA was extracted from all samples and libraries were constructed. This was followed by sequencing using the Illumina sequencing platform, and results were studied using a biological information data analysis process. We divided the data into two groups based on progression‐free survival (PFS) ≥ six months and PFS

The intestinal microbiota plays an important role in the health and metabolism of the host. Next‐generation sequencing technology has enabled the characterization of the gut microbiota of several animal species. We analyzed the intestinal microbiota in six different parts of the gastrointestinal tracts (GITs) of five Mongolian horses by sequencing the 16S rRNA gene V3‐V4 hypervariable region. All horses were kept in the natural habitat of the Inner Mongolia grassland. Significant differences were observed among the microbiota compositions of the distinct GIT regions. In addition, while the microbial community structures of the small and large intestine were significantly different, those of the cecum and colon were similar. In the foregut, Firmicutes (65%) and Proteobacteria (23%) were the most abundant, while Firmicutes (45%) and Bacteroidetes (42%) were the most common in the hindgut. At the level of family, Ruminococcaceae (p = .203), Lachnospiraceae (p = .157), Rikenellaceae (p = .122), and Prevotellaceae (p = .068) were predominant in the hindgut, while the relative abundance of the Akkermansia genus (5.7%, p = .039) was higher in the ventral colon. In terms of the putative functions, the ratio of microbial abundance in the different parts of the GIT was similar, the result can help characterize the gut microbial structure of different animals., The microbial communities of the different parts of the Mongolian horse gastrointestinal tracts were significantly different, and there was greater diversity between the lower gut and upper gut. Direct sampling of the different segments of gastrointestinal tracts provided a more complete diagram of the gut microbiota than fecal analysis. The vegetarian diets and adaptability of Mongolian horses were likely related not only to their stable and complicated gastrointestinal microbiota but also to their special herbivorous digestive physiology.

Noninvasive sampling methods for studying intestinal microbiomes are widely applied in studies of endangered species and in those conducting temporal monitoring during manipulative experiments. Although existing studies show that noninvasive sampling methods among different taxa vary in their accuracy, no studies have yet been published comparing nonlethal sampling methods in adult amphibians. In this study, we compare microbiomes from two noninvasive sample types (faeces and cloacal swabs) to that of the large intestine in adult cane toads, Rhinella marina. We use 16S rRNA gene sequencing to investigate how microbial communities change along the digestive tract and which nonlethal sampling method better represents large intestinal microbiota. We found that cane toads' intestinal microbiota was dominated by Bacteroidetes, Proteobacteria and Firmicutes and, interestingly, we also saw a high proportion of Fusobacteria, which has previously been associated with marine species and changes in frog immunity. The large and small intestine of cane toads had a similar microbial composition, but the large intestine showed higher diversity. Our results indicate that cloacal swabs were more similar to large intestine samples than were faecal samples, and small intestine samples were significantly different from both nonlethal sample types. Our study provides valuable information for future investigations of the cane toad gut microbiome and validates the use of cloacal swabs as a nonlethal method to study changes in the large intestine microbiome. These data provide insights for future studies requiring nonlethal sampling of amphibian gut microbiota.

Members of the Bacteroidetes phylum, represented by Alistipes finegoldii, are prominent anerobic, Gram-negative inhabitants of the gut microbiome. The lipid biosynthetic pathways were analyzed using bioinformatic analyses, lipidomics, metabolic labeling and biochemistry to characterize exogenous fatty acid metabolism. A. finegoldii only produced the saturated fatty acids. The most abundant lipids were phosphatidylethanolamine (PE) and sulfonolipid (SL). Neither phosphatidylglycerol nor cardiolipin are present. PE synthesis is initiated by the PlsX/PlsY/PlsC pathway, whereas the SL pathway is related to sphingolipid biosynthesis. A. finegoldii incorporated medium-chain fatty acids (≤14 carbons) into PE and SL after their elongation, whereas long-chain fatty acids (≥16 carbons) were not elongated. Fatty acids >16 carbons were primarily incorporated into the 2-position of phosphatidylethanolamine at the PlsC step, the only biosynthetic enzyme that utilizes long-chain acyl-ACP. The ability to assimilate a broad-spectrum of fatty acid chain lengths present in the gut environment is due to the expression of two acyl-acyl carrier protein (ACP) synthetases. Acyl-ACP synthetase 1 had a substrate preference for medium-chain fatty acids and synthetase 2 had a substrate preference for long-chain fatty acids. This unique combination of synthetases allows A. finegoldii to utilize both the medium- and long-chain fatty acid nutrients available in the gut environment to assemble its membrane lipids.

Ocean pollution is a worldwide environmental challenge that could be partially tackled through microbial applications. To shed light on the diversity and applications of the bacterial communities that inhabit the sediments trapped in artificial containers, we analyzed residues (polyethylene terephthalate [PET] bottles and aluminum cans) collected from the Mediterranean Sea by scanning electron microscopy and next generation sequencing. Moreover, we set a collection of culturable bacteria from the plastisphere that were screened for their ability to use PET as a carbon source. Our results reveal that Proteobacteria are the predominant phylum in all the samples and that Rhodobacteraceae, Woeseia, Actinomarinales, or Vibrio are also abundant in these residues. Moreover, we identified marine isolates with enhanced growth in the presence of PET: Aquimarina intermedia, Citricoccus spp., and Micrococcus spp. Our results suggest that the marine environment is a source of biotechnologically promising bacterial isolates that may use PET or PET additives as carbon sources., Financial support by Ministerio de Ciencia e Innovación (grant SETH ref. RTI2018‐095584‐B‐C41‐42‐43‐44 co‐financed by FEDER), the European Union H2020 (BIOROBOOST project ID 210491758; Micro4Biogas project ref.101000470), Agencia Estatal de la Innovación AEI (MIPLACE projectref. PCI2019‐111845‐2), and Agència Valenciana de la Innovación AVI (ENTOMOPLAST project ref. INNEST/2021/334) are acknowl-edged. Àngela Vidal‐Verdú and Esther Molina‐Menor are funded with a Formación del Profesorado Universitario grant from the Spanish Ministerio de Ciencia, Innovación y Universidades with references FPU18/02578 and FPU17/04184, respectively. Adriel Latorre‐Pérezis a recipient of a Doctorado Industrial fellowship from the Spanish Ministerio de Ciencia, Innovación y Universidades (reference DI‐17‐09613).

Ginsenosides, including Rb1 , Rb2 , Rb3 and Rc, belong to protopanaxadiol-type saponins in Panax ginseng C. A. Mey. Their contents are high in P. ginseng. They could inhibit oxidant stress, enhance immunity, lower blood sugar, resist tumor cells and facilitate other physiological activities. This study aimed to explore the interaction between ginsenosides Rb1 , Rb2 , Rb3 and Rc and the intestinal flora of healthy people. It also sought to analyse the biotransformation products and pathways of these ginsenosides in in-vitro human intestinal bacteria and their effects on the diversity of human intestinal flora. Human intestinal bacteria were incubated with ginsenosides Rb1 , Rb2 , Rb3 and Rc at 37 °C under anaerobic conditions. Samples were taken at different timepoints. The transformed products were identified by rapid high-resolution liquid chromatography-quadrupole time-of-flight mass spectrometry. After 48 h of transformation, the transformed product of ginsenosides Rb1 , Rb2 , Rb3 and Rc was ginsenoside compound K. The transformation rates were 83.5 %, 88.7 %, 85.6 %, and 84.2 %. 16S rRNA sequencing technology was applied to the bioinformatic analysis of faecal samples incubated for 48 h. Relative to the blank control, the relative abundance of Firmicutes and Proteobacteria significantly increased at the phylum level. Moreover, the relative abundance of Bacteroidetes significantly decreased in ginsenosides Rb1 , Rb2 , Rb3 and Rc. At the genus level, the relative abundance of Escherichia significantly increased, whereas that of Dorea, Prevotella and Megasphaera significantly decreased in all groups. These results showed that Rb1 , Rb2 , Rb3 and Rc could improve the structure and diversity of human intestinal flora and balance the metabolic process.

Gut microbiota disorder will lead to intestinal damage. This study evaluated the influence of total diterpenoids extracted from Euphorbia pekinensis (TDEP) on gut microbiota and intestinal mucosal barrier after long‐term administration, and the correlations between gut microbiota and intestinal mucosal barrier were analysed by Spearman correlation analysis. Mice were randomly divided to control group, TDEP groups (4, 8, 16 mg/kg), TDEP (16 mg/kg) + antibiotic group. Two weeks after intragastric administration, inflammatory factors (TNF‐α, IL‐6, IL‐1β) and LPS in serum, short chain fatty acids (SCFAs) in feces were tested by Enzyme‐linked immunosorbent assay (ELISA) and high‐performance liquid chromatography (HPLC), respectively. The expression of tight junction (TJ) protein in colon was measured by western blotting. Furthermore, the effects of TDEP on gut microbiota community in mice have been investigated by 16SrDNA high‐throughput sequencing. The results showed TDEP significantly increased the levels of inflammatory factors in dose‐dependent manners, and decreased the expression of TJ protein and SCFAs, and the composition of gut microbiota of mice in TDEP group was significantly different from that of control group. When antibiotics were added, the diversity of gut microbiota was significantly reduced, and the colon injury was more serious. Finally, through correlation analysis, we have found nine key bacteria (Barnesiella, Muribaculaceae_unclassified, Alloprevotella, Candidatus_Arthromitus, Enterorhabdus, Alistipes, Bilophila, Mucispirillum, Ruminiclostridium) that may be related to colon injury caused by TDEP. Taken together, the disturbance of gut microbiota caused by TDEP may aggravate the colon injury, and its possible mechanism may be related to the decrease of SCFAs in feces, disrupted the expression of TJ protein in colon and increasing the contents of inflammatory factors., The total diterpenoids were extracted and isolated from the radix of Euphorbia pekinensis (TDEP), and it’s influence on gut microbiota and intestinal mucosal barrier were evaluated. Correlation analysis was conducted to find out key microbiota. In conclusion, we found the disturbance of gut microbiota caused by TDEP may aggravate the colon injury, and its possible mechanism may be related to the decrease of SCFAs in feces, disrupted the expression of TJ protein in colon and increasing the contents of inflammatory factors.

Marine biofouling imposes serious environmental and economic impacts on marine applications, especially in the shipping industry. To combat biofouling, protective coatings are applied on vessel hulls which are divided into two major groups: biocidal and non‐toxic fouling release. The current study aimed to explore the effect of coating type on microbial biofilm community profiles to better understand the differences between the communities developed on fouling control biocidal antifouling and biocidal‐free coatings. Biocidal (Intersmooth® 7460HS SPC), fouling release (Intersleek® 900), and inert surfaces were deployed in the marine environment for 4 months, and the biofilms that developed on these surfaces were investigated using Illumina NGS sequencing, targeting the prokaryotic 16S rRNA gene. The results confirmed differences in the community profiles between coating types. The biocidal coating supported communities dominated by Alphaproteobacteria (Loktanella, Sphingorhabdus, Erythrobacter) and Bacteroidetes (Gilvibacter), while other taxa, such as Portibacter and Sva0996 marine group, proliferated on the fouling‐release surface. Knowledge of these marine biofilm components on fouling control coatings will serve as a guide for future investigations of marine microfouling as well as informing the coatings industry of potential microbial targets for robust coating formulations., Marine biofilms constitute the pioneering components of biofouling, a phenomenon with significant environmental and economic impacts in maritime applications. Antifouling control strategies are applied on vessel hulls based on the application of protective paints. Here, we explored the in situ prokaryotic biofilm community composition and abundance on different types of commercial fouling control coatings (fouling release, biocidal) employing next‐generation sequencing targeting the 16S rRNA gene. Our results indicated distinct microbial community profiles between coating types, with specific genera contributing to differences between surfaces.