Massive expansion of human gut bacteriophage diversity.

Bacteriophages drive evolutionary change in bacterial communities by creating gene flow networks that fuel ecological adaptions. However, the extent of viral diversity and its prevalence in the human gut remains largely unknown. Here, we introduce the Gut Phage Database, a collection of ∼142,000 non-redundant viral genomes (>10 kb) obtained by mining a dataset of 28,060 globally distributed human gut metagenomes and 2,898 reference genomes of cultured gut bacteria. Host assignment revealed that viral diversity is highest in the Firmicutes phyla and that ∼36% of viral clusters (VCs) are not restricted to a single species, creating gene flow networks across phylogenetically distinct bacterial species. Epidemiological analysis uncovered 280 globally distributed VCs found in at least 5 continents and a highly prevalent phage clade with features reminiscent of p-crAssphage. This high-quality, large-scale catalog of phage genomes will improve future virome studies and enable ecological and evolutionary analysis of human gut bacteriophages.

Mining the Human Gut Microbiota for Immunomodulatory Organisms.

Within the human gut reside diverse microbes coexisting with the host in a mutually advantageous relationship. Evidence has revealed the pivotal role of the gut microbiota in shaping the immune system. To date, only a few of these microbes have been shown to modulate specific immune parameters. Herein, we broadly identify the immunomodulatory effects of phylogenetically diverse human gut microbes. We monocolonized mice with each of 53 individual bacterial species and systematically analyzed host immunologic adaptation to colonization. Most microbes exerted several specialized, complementary, and redundant transcriptional and immunomodulatory effects. Surprisingly, these were independent of microbial phylogeny. Microbial diversity in the gut ensures robustness of the microbiota's ability to generate a consistent immunomodulatory impact, serving as a highly important epigenetic system. This study provides a foundation for investigation of gut microbiota-host mutualism, highlighting key players that could identify important therapeutics.

Gut bacteria are essential for development of an invasive bark beetle by regulating glucose transport.

Insects and their gut bacteria form a tight and beneficial relationship, especially in utilization of host nutrients. The red turpentine beetle (RTB), a destructive and invasive pine pest, employs mutualistic microbes to facilitate its invasion success. However, the molecular mechanism underlying the utilization of nutrients remains unknown. In this study, we found that gut bacteria are crucial for the utilization of D-glucose, a main carbon source for RTB development. Downstream assays revealed that gut bacteria-induced gut hypoxia and the secretion of riboflavin are responsible for RTB development by regulating D-glucose transport via the activation of a hypoxia-induced transcription factor 1 (Hif-1α). Further functional investigations confirmed that Hif-1α mediates glucose transport by direct upregulation of two glucose transporters (ST10 and ST27), thereby promoting RTB development. Our findings reveal how gut bacteria regulate the development of RTB, and promote our understanding of the mutualistic relationship of animals and their gut bacteria.

Outer Membrane Vesicles Released from Garlic Exosome-like Nanoparticles (GaELNs) Train Gut Bacteria that Reverses Type 2 Diabetes via the Gut-Brain Axis.

Gut microbiota function has numerous effects on humans and the diet humans consume has emerged as a pivotal determinant of gut microbiota function. Here, a new concept that gut microbiota can be trained by diet-derived exosome-like nanoparticles (ELNs) to release healthy outer membrane vesicles (OMVs) is introduced. Specifically, OMVs released from garlic ELN (GaELNs) trained human gut Akkermansia muciniphila (A. muciniphila) can reverse high-fat diet-induced type 2 diabetes (T2DM) in mice. Oral administration of OMVs released from GaELNs trained A. muciniphila can traffick to the brain where they are taken up by microglial cells, resulting in inhibition of high-fat diet-induced brain inflammation. GaELNs treatment increases the levels of OMV Amuc-1100, P9, and phosphatidylcholines. Increasing the levels of Amuc-1100 and P9 leads to increasing the GLP-1 plasma level. Increasing the levels of phosphatidylcholines is required for inhibition of cGas and STING-mediated inflammation and GLP-1R crosstalk with the insulin pathway that leads to increasing expression of Insulin Receptor Substrate (IRS1 and IRS2) on OMV targeted cells. These findings reveal a molecular mechanism whereby OMVs from plant nanoparticle-trained gut bacteria regulate genes expressed in the brain, and have implications for the treatment of brain dysfunction caused by a metabolic syndrome.

Gut microbes on the risk of advanced adenomas.

BACKGROUND: More than 90% of colorectal cancer (CRC) arises from advanced adenomas (AA) and gut microbes are closely associated with the initiation and progression of both AA and CRC. OBJECTIVE: To analyze the characteristic microbes in AA. METHODS: Fecal samples were collected from 92 AA and 184 negative control (NC). Illumina HiSeq X sequencing platform was used for high-throughput sequencing of microbial populations. The sequencing results were annotated and compared with NCBI RefSeq database to find the microbial characteristics of AA. R-vegan package was used to analyze α diversity and ß diversity. α diversity included box diagram, and ß diversity included Principal Component Analysis (PCA), principal co-ordinates analysis (PCoA), and non-metric multidimensional scaling (NMDS). The AA risk prediction models were constructed based on six kinds of machine learning algorithms. In addition, unsupervised clustering methods were used to classify bacteria and viruses. Finally, the characteristics of bacteria and viruses in different subtypes were analyzed. RESULTS: The abundance of Prevotella sp900557255, Alistipes putredinis, and Megamonas funiformis were higher in AA, while the abundance of Lilyvirus, Felixounavirus, and Drulisvirus were also higher in AA. The Catboost based model for predicting the risk of AA has the highest accuracy (bacteria test set: 87.27%; virus test set: 83.33%). In addition, 4 subtypes (B1V1, B1V2, B2V1, and B2V2) were distinguished based on the abundance of gut bacteria and enteroviruses (EVs). Escherichia coli D, Prevotella sp900557255, CAG-180 sp000432435, Phocaeicola plebeiuA, Teseptimavirus, Svunavirus, Felixounavirus, and Jiaodavirus are the characteristic bacteria and viruses of 4 subtypes. The results of Catboost model indicated that the accuracy of prediction improved after incorporating subtypes. The accuracy of discovery sets was 100%, 96.34%, 100%, and 98.46% in 4 subtypes, respectively. CONCLUSION: Prevotella sp900557255 and Felixounavirus have high value in early warning of AA. As promising non-invasive biomarkers, gut microbes can become potential diagnostic targets for AA, and the accuracy of predicting AA can be improved by typing.

Third-generation PacBio sequencing to explore gut bacteria and gender in colorectal cancer.

BACKGROUND: Gut bacteria have an important influence on colorectal cancer (CRC). The differences of gut bacteria between genders have been the hot spots. OBJECTIVE: To analyze the relationship between gut bacteria and gender differences in patients with CRC. METHODS: A total of 212 patients with CRC and 212 healthy volunteers were recruited. The subjects' fecal samples were obtained, and the fecal microorganisms were analyzed by the third-generation sequencing PacBio. The composition of gut bacteria was analyzed. Linear discriminant analysis Effect Size (LEfSe) was used to analyze the differences in gut bacteria. Pearson coefficient was used to calculate the correlation between differential bacteria. CRC risk prediction models were used to rank the importance of effective differential bacteria. RESULTS: Escherichia flexneri and Phocaeicola vulgatus were the most frequent bacteria in both male and female CRC patients. Bacteroides, Verrucomicrobia and Akkermansiaceae were highly enriched in male CRC group, while Bacteroidetes, Phocaeicola and Tissierellales were highly enriched in female CRC group. Peptostreptococcus anaerobius and Phocaeicola vulgatus were important CRC related bacteria in males and females, respectively. Peptostreptococcus anaerobius was the most important characteristic bacterium of males (AUC = 0.951), and the sensitivity and specificity of the discovery set were 78.74 % and 93.98 %, respectively. Blautia stercoris was the most important characteristic bacterium of females (AUC = 0.966), and the sensitivity and specificity of the discovery set were 90.63 % and 90.63 %, respectively. CONCLUSION: Gut bacteria varied in different genders. Therefore, gender should be considered when gut bacteria are applied in the diagnose and prevention of CRC.

Effects of gut bacteria and their metabolites on gut health of animals.

The intestine tract is a vital site for the body to acquire nutrients, serving as the largest immune organ. Intestinal health is crucial for maintaining a normal physiological state. Abundant microorganisms reside in the intestine, colonized in a symbiotic manner. These microorganisms can generate various metabolites that influence host physiological activities. Microbial metabolites serve as signaling molecules or metabolic substrates in the intestine, and some intestinal microorganisms act as probiotics and promote intestinal health. Researches on host, probiotics, microbial metabolites and their interactions are ongoing. This study reviews the effects of gut bacteria and their metabolites on intestinal health to provide useful references for animal husbandry.

Microbial ensemble in the hives: deciphering the intricate gut ecosystem of hive and forager bees of Apis mellifera.

BACKGROUND: The gut microbiome of honey bees significantly influences vital traits and metabolic processes, including digestion, detoxification, nutrient provision, development, and immunity. However, there is a limited information is available on the gut bacterial diversity of western honey bee populations in India. This study addresses the critical knowledge gap and outcome of which would benefit the beekeepers in India. METHODS AND RESULTS: This study investigates the gut bacterial diversity in forager and hive bees of Indian Apis mellifera, employing both culture-based and culture-independent methods. In the culturable study, a distinct difference in gut bacterial alpha and beta diversity between forager and hive bees emerges. Firmicutes, Proteobacteria, and Actinobacteria dominate, with hive bees exhibiting a Firmicutes-rich gut (65%), while foragers showcase a higher proportion of Proteobacteria (37%). Lactobacillus in the hive bee foregut aligns with the findings by other researchers. Bacterial amplicon sequencing analysisreveals a more intricate bacterial composition with 18 identified phyla, expanding our understanding compared to culturable methods. Hive bees exhibit higher community richness and diversity, likely due to diverse diets and increased social interactions. The core microbiota includes Snodgrassella alvi, Gilliamella apicola, and Bombilactobacillus mellis and Lactobacillus helsingborgensis, crucial for digestion, metabolism, and pathogen resistance. The study emphasises bacteria's role in pollen and nectar digestion, with specific groups like Lactobacillus and Bifidobobacterium spp. associated with carbohydrate metabolism and polysaccharide breakdown. These microbes aid in starch and sucrose digestion, releasing beneficial short-chain fatty acids. CONCLUSION: This research highlights the intricate relationship between honey bees and their gut microbiota, showcasing how the diverse and complex microbiome helps bees overcome dietary challenges and enhances overall host health. Understanding these interactions contributes to bee ecology knowledge and has implications for honey bee health management, emphasising the need for further exploration and conservation efforts.

Investigating the influence of the gut microbiome on cholelithiasis: unveiling insights through sequencing and predictive modeling.

BACKGROUND: Cholelithiasis is one of the most common disorders of hepatobiliary system. Gut bacteria may be involved in the process of gallstone formation and are, therefore considered as potential targets for cholelithiasis prediction. OBJECTIVE: To reveal the correlation between cholelithiasis and gut bacteria. METHODS: Stool samples were collected from 100 cholelithiasis and 250 healthy individuals from Huzhou Central Hospital; The 16S rRNA of gut bacteria in the stool samples was sequenced using the third-generation Pacbio sequencing platform; Mothur v.1.21.1 was used to analyze the diversity of gut bacteria; Wilcoxon rank-sum test and linear discriminant analysis of effect sizes (LEfSe) were used to analyze differences in gut bacteria between patients suffering from cholelithiasis and healthy individuals; Chord diagram and Plot-related heat maps were used to analyze the correlation between cholelithiasis and gut bacteria; six machine algorithms were used to construct models to predict cholelithiasis. RESULTS: There were differences in the abundance of gut bacteria between cholelithiasis and healthy individuals, but there were no differences in their community diversity. Increased abundance of Costridia, Escherichia flexneri, and Klebsiella pneumonae were found in cholelithiasis, while Bacteroidia, Phocaeicola, and Phocaeicola vulgatus were more abundant in healthy individuals. The top four bacteria that were most closely associated with cholelithiasis were Escherichia flexneri, Escherichia dysenteriae, Streptococcus salivarius, and Phocaeicola vulgatus. The cholelithiasis model based on CatBoost algorithm had the best prediction effect (sensitivity: 90.48%, specificity: 88.32%, and AUC: 0.962). CONCLUSION: The identification of characteristic gut bacteria may provide new predictive targets for gallstone screening. As being screened by the predictive model, people at high risk of cholelithiasis can determine the need for further testing, thus enabling early warning of cholelithiasis.

Pharmacokinetics, mass balance, tissue distribution, metabolism, and excretion of [14C]aficamten following single oral dose administration to rats.

The pharmacokinetics, metabolism, excretion, mass balance, and tissue distribution of [14C]aficamten were evaluated following oral administration of an 8 mg/kg dose in Sprague Dawley rats and in a quantitative whole-body autoradiography study in Long Evans rats.[14C]Aficamten accounted for ∼80% and a hydroxylated metabolite (M1) accounted for ∼12% of total radioactivity in plasma over 48-h (AUC0-48). Plasma tmax was 4-h and the t1/2 of total plasma radioactivity was 5.8-h.Tissues showing highest Cmax exposures were myocardium and semitendinosus muscle.Most [14C]aficamten-derived radioactivity was excreted within 48-h post-administration. Mean cumulative recovery in urine and faeces over 168-h was 8.3% and 90.7%, respectively.In urine and bile, unchanged aficamten was detected at <0.1 and <0.2% of dose, respectively; however, based on total radioactivity excreted in urine (8.0%) and bile (51.7%), approximately 60% of dose was absorbed.[14C]Aficamten was metabolised by hydroxylation with subsequent glucuronidation where the most abundant metabolite recovered in bile was M5 (35.2%), the oxygen-linked glucuronide of hydroxylated aficamten (M1a). The major metabolite detected in faeces was a 1,2,4-oxadiazole moiety ring-cleaved metabolite (M18, 35.3%), shown to be formed from the metabolism of M5 in incubations with rat intestinal contents solution.

Isolation and characterization of bio-prospecting gut strains Bacillus safensis CGK192 and Bacillus australimaris CGK221 for plastic (HDPE) degradation.

The present work reports the application of novel gut strains Bacillus safensis CGK192 (Accession No. OM658336) and Bacillus australimaris CGK221 (Accession No. OM658338) in the biological degradation of synthetic polymer i.e., high-density polyethylene (HDPE). The biodegradation assay based on polymer weight loss was conducted under laboratory conditions for a period of 90 days along with regular evaluation of bacterial biomass in terms of total protein content and viable cells (CFU/cm2). Notably, both strains achieved significant weight reduction for HDPE films without any physical or chemical pretreatment in comparison to control. Hydrophobicity and biosurfactant characterization were also done in order to assess strains ability to form bacterial biofilm over the polymer surface. The post-degradation characterization of HDPE was also performed to confirm degradation using analytical techniques such as Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), Field emission scanning electronic microscopy (FE-SEM) coupled with energy dispersive X-ray (EDX), and Gas chromatography-mass spectrometry (GC-MS). Interestingly strain CGK221 was found to be more efficient in forming biofilm over polymer surface as indicated by lower half-life (i.e., 0.00032 day-1) and higher carbonyl index in comparison to strain CGK192. The findings reflect the ability of our strains to develop biofilm and introduce an oxygenic functional group into the polymer surface, thereby making it more susceptible to degradation.

Plasma Concentrations of Trimethylamine-N-Oxide, Choline, and Betaine in Patients With Moderate to Advanced Chronic Kidney Disease and Their Relation to Cardiovascular and Renal Outcomes.

OBJECTIVES: Trimethylamine N-oxide (TMAO) is a gut bacteria-mediated liver metabolite of dietary betaine, choline, and carnitine, which is excreted by glomerular filtration. We studied whether TMAO is excreted by cardiovascular disease (CVD) in patients with chronic kidney disease (CKD). METHODS: Among 478 patients with CKD stage G2 (n = 104), G3a (n = 163), G3b (n = 123), and G4 (n = 88), we studied the association between fasting plasma concentrations of TMAO, choline, or betaine at baseline and kidney function, prevalent CVD, and future renal outcomes during a mean follow-up of 5.1 years. RESULTS: Decreased glomerular filtration rate was associated with higher plasma concentrations of TMAO, choline, and betaine. Baseline concentrations of TMAO were higher in participants with preexisting CVD compared to those without CVD (8.4 [10.1] vs. 7.8 [8.0] µmol/L; P = .047), but the difference was not significant after adjusting for confounders. During the follow-up, 147 participants experienced CVD or died, and 144 reached the predefined renal endpoint. In the adjusted regression analyses, TMAO or choline concentrations in the upper three quartiles (vs. the lowest quartile) were not associated with any of the study's clinical endpoints. In contrast, the adjusted hazard ratio of plasma betaine in the highest quartile versus the lowest quartile was 2.14 (1.32, 3.47) for the CVD endpoint and 1.64 (1.00, 2.67) for the renal endpoint. CONCLUSIONS: Elevated plasma TMAO concentrations were explained by impaired kidney function. Elevated plasma concentrations of betaine, but not those of TMAO or choline, constituted a risk factor for adverse outcomes. TMAO might not be an appropriate target to reduce CVD or renal outcomes in patients with preexisting CKD.

Gut bacterium Burkholderia cepacia (BsNLG8) and immune gene Defensin A contribute to the resistance against Nicotine-induced stress in Nilaparvata lugens (Stål).

Nicotine, a naturally occurring alkaloid found in tobacco, is a potent neurotoxin extensively used to control Nilaparvata lugens (Stål), a destructive insect pest of rice crops. The insect gut harbors a wide array of resident microorganisms that profoundly influence several biological processes, including host immunity. Maintaining an optimal gut microbiota and immune homeostasis requires a complex network of reciprocal regulatory interactions. However, the underlying molecular mechanisms driving these symbiotic exchanges, particularly between specific gut microbe and immunity, remain largely unknown in insects. Our previous investigations identified and isolated a nicotine-degrading Burkholderia cepacia strain (BsNLG8) with antifungal properties. Building on those findings, we found that nicotine intake significantly increased the abundance of a symbiotic bacteria BsNLG8, induced a stronger bacteriostatic effect in hemolymph, and enhanced the nicotine tolerance of N. lugens. Additionally, nicotine-induced antimicrobial peptides (AMPs) exhibited significant antibacterial effects against Staphylococcus aureus. We adopted RNA-seq to explore the underlying immunological mechanisms in nicotine-stressed N. lugens. Bioinformatic analyses identified numerous differentially expressed immune genes, including recognition/immune activation (GRPs and Toll) and AMPs (i.e., Defensin, Lugensin, lysozyme). Temporal expression profiling (12, 24, and 48 hours) of immune genes revealed pattern recognition proteins and immune effectors as primary responders to nicotine-induced stress. Defensin A, a broad-spectrum immunomodulatory cationic peptide, exhibited significantly high expression. RNA interference-mediated silencing of Defensin A reduced the survival, enhanced nicotine sensitivity of N. lugens to nicotine, and decreased the abundance of BsNLG8. The reintroduction of BsNLG8 improved the expression of immune genes, aiding nicotine resistance of N. lugens. Our findings indicate a potential reciprocal immunomodulatory interaction between Defensin A and BsNLG8 under nicotine stress. Moreover, this study offers novel and valuable insights for future research into enhancing nicotine-based pest management programs and developing alternative biocontrol methods involving the implication of insect symbionts.

Effects of tefluthrin and guadipyr on the midgut bacteria of adult Apis mellifera.

The objective of this study is to assess the potential impact of tefluthrin and guadipyr on the gut microbial composition and metabolism in adult Apis mellifera ligustica, thereby elucidating the underlying mechanisms of insecticide action and its practical implications for bee protection. In this investigation, A. mellifera were subjected to one of three dietary conditions: (1) control sugar water, (2) tefluthrin-infused sugar water, or (3) guadipyr-infused sugar water. After a 10-day exposure period, genomic DNA from the gut bacteria was extracted. High-throughput sequencing was employed to evaluate the potential influence of tefluthrin and guadipyr treatments on the diversity and abundance of gut bacteria. Among the A. mellifera specimens, a total of twenty species of gut bacteria were identified, spanning across five phyla, six classes, eleven orders, eleven families, and fifteen genera. The dominant phyla within the gut bacterial community were Proteobacteria and Bacteroidetes. In comparison to the control group, both the tefluthrin-treated and deltamethrin-treated groups exhibited alterations in the composition of their gut bacterial flora. At the phylum level, there was a significant decrease in the relative abundance of Cyanobacteria (P < 0.05). On the genus level, the tefluthrin group displayed a significant increase in the relative abundance of Bartonella and Serratia (P < 0.05). In the guadipyr-treated group, the relative abundance of Gilliamella and Frischella increased significantly (P < 0.05), while the relative abundance of norank_o_Chloroplast and Enterobacter decreased significantly (P < 0.05). Further analysis of cluster of orthologous genes predicted functional changes in gut microbial metabolism following tefluthrin exposure but no significant changes after guadipyr exposure. Consequently, exposure to tefluthrin and guadipyr can induce shifts in both the composition and metabolic activity of the gut bacteria in A. mellifera. Notably, the impact of tefluthrin on the gut bacteria of A. mellifera appears to be more pronounced compared to that of guadipyr.

Impact of a Functional Dairy Powder and Its Primary Component on the Growth of Pathogenic and Probiotic Gut Bacteria and Human Coronavirus 229E.

Milk boasts an array of potent bioactive compounds, such as lactoferrin (Lf), immunoglobulins, and functional proteins, all delivering substantial therapeutic benefits. In this study, Immune Powder (a functional dairy formulation) and its primary component called Fractionated Milk Protein (FMP) containing Lf, zinc, and immunoglobulins and formulated by Ausnutria Pty Ltd. were evaluated for their potential broad-spectrum pharmacological activity. In particular, this study investigated the antibacterial (against pathogenic Escherichia coli), prebiotic (promoting Lactobacillus delbrueckii growth), anti-inflammatory (inhibition of NO production in RAW264.7 macrophages), and antiviral (against human coronavirus 229E) effects of the samples. In addition, the impact of simulated gastric digestion on the efficacy of the samples was explored. LCMS-based proteomics was implemented to unveil cellular and molecular mechanisms underlying antiviral activity. The Immune Powder demonstrated antibacterial activity against E. coli (up to 99.74 ± 11.47% inhibition), coupled with prebiotic action (10.84 ± 2.2 viability fold-change), albeit these activities diminished post-digestion (p < 0.01). The Immune Powder effectively mitigated NO production in lipopolysaccharide-stimulated RAW264.7 macrophages, with declining efficacy post-digestion (p < 0.0001). The Immune Powder showed similar antiviral activity before and after digestion (p > 0.05) with up to 3-fold improvement. Likewise, FMP exhibited antibacterial potency pre-digestion at high concentrations (95.56 ± 1.23% inhibition at 125 mg/mL) and post-digestion at lower doses (61.82 ± 5.58% inhibition at 3906.25 µg/mL). FMP also showed enhanced prebiotic activity post-digestion (p < 0.0001), NO inhibition pre-digestion, and significant antiviral activity. The proteomics study suggested that the formulation and its primary component shared similar antiviral mechanisms by inhibiting scavenger receptor binding and extracellular matrix interaction.

The Bee Gut Microbiota: Bridging Infective Agents Potential in the One Health Context.

The bee gut microbiota plays an important role in the services the bees pay to the environment, humans and animals. Alongside, gut-associated microorganisms are vehiculated between apparently remote habitats, promoting microbial heterogeneity of the visited microcosms and the transfer of the microbial genetic elements. To date, no metaproteomics studies dealing with the functional bee microbiota are available. Here, we employ a metaproteomics approach to explore a fraction of the bacterial, fungal, and unicellular parasites inhabiting the bee gut. The bacterial community portrays a dynamic composition, accounting for specimens of human and animal concern. Their functional features highlight the vehiculation of virulence and antimicrobial resistance traits. The fungal and unicellular parasite fractions include environment- and animal-related specimens, whose metabolic activities support the spatial spreading of functional features. Host proteome depicts the major bee physiological activities, supporting the metaproteomics strategy for the simultaneous study of multiple microbial specimens and their host-crosstalks. Altogether, the present study provides a better definition of the structure and function of the bee gut microbiota, highlighting its impact in a variety of strategies aimed at improving/overcoming several current hot topic issues such as antimicrobial resistance, environmental pollution and the promotion of environmental health.

Comparative Analysis of Gut Bacterial Community Composition in Two Tropical Economic Sea Cucumbers under Different Seasons of Artificial Environment.

With the continuous rise of the sea cucumber aquaculture industry in China, the tropical sea cucumber aquaculture industry is also improving. However, research on the gut microorganisms of tropical sea cucumbers in captivity is scarce. In this study, high-throughput sequencing methods were used to analyze the gut microbial composition of Stichopus monotuberculatus and Holothuria scabra in the dry season and wet season of artificial environments. The results showed that 66 phyla were obtained in all samples, of which 59 phyla were obtained in the dry season, and 45 phyla were obtained in the wet season. The Tax4Fun analysis showed that certain gut bacterial communities affect the daily metabolism of two sea cucumber species and are involved in maintaining gut microecological balance in the gut of two sea cucumber species. In addition, compared with differences between species, PCoA and UPGMA clustering analysis showed the gut prokaryotes of the same sea cucumber species varied more in different seasons, indicating that the influence of environment was higher than the feeding choices of sea cucumbers under relatively closed conditions. These results revealed the gut bacterial community composition of S. monotuberculatus and H. scabra and the differences in gut bacterial structure between two sea cucumber species in different seasons were compared, which would provide the foundation for tropical sea cucumber aquaculture in the future.

Beneficial Effects of Dietary Fiber in Young Barley Leaf on Gut Microbiota and Immunity in Mice.

The health benefits of young barley leaves, rich in dietary fiber, have been studied for several decades; however, their beneficial effects on the intestinal microenvironment remain to be elucidated. To investigate the effects of young barley leaf-derived dietary fiber (YB) on the gut microbiota and immunity, mice were fed an AIN-93G diet containing cellulose or YB and subjected to subsequent analysis. The population of MHC-II-positive conventional dendritic cells (cDCs) and CD86 expression in the cDCs of Peyer's patches were elevated in the YB-fed mice. MHC-II and CD86 expression was also elevated in the bone marrow-derived DCs treated with YB. 16S-based metagenomic analysis revealed that the gut microbiota composition was markedly altered by YB feeding. Among the gut microbiota, Lachnospiraceae, mainly comprising butyrate-producing NK4A136 spp., were overrepresented in the YB-fed mice. In fact, fecal butyrate concentration was also augmented in the YB-fed mice, which coincided with increased retinaldehyde dehydrogenase (RALDH) activity in the CD103+ cDCs of the mesenteric lymph nodes. Consistent with elevated RALDH activity, the population of colonic IgA+ plasma cells was higher in the YB-fed mice than in the parental control mice. In conclusion, YB has beneficial effects on the gut microbiota and intestinal immune system.

Modulation of Human Gut Microbiota In Vitro by Inulin-Type Fructan from Codonopsis pilosula Roots.

Inulin-type fructan (ITF) defined as a polydisperse carbohydrate consisting mainly of ß-(2-1) fructosyl-fructose links exerts potential prebiotics properties by selectively stimulating the growth of Bifidobacterium and Lactobacillus. This study reported the modulation of human gut microbiota in vitro by ITF from Codonopsis pilosula roots using 16S ribosomal RNA gene sequencing. The microbiota community structure analysis at genus levels showed that 50 mg/mL ITF significantly stimulated the growth of Prevotella and Faecalibacterium. LEfSe analysis showed that ITF at 25 and 50 mg/mL primarily increased the relative abundance of genera Parabacteroides and Alistipes (LDA Score > 4), and genera Prevotella and Faecalibacterium (LDA Score > 4) as well as Acidaminococcus, Megasphaera, Bifidobacterium and Megamonas (LDA Score > 3.5), respectively. Meanwhile, ITF at 25 and 50 mg/mL exhibited the effects of lowering pH values of samples after 24 h fermentation (p < 0.05). The results indicated that ITF likely has potential in stimulating the growth of Prevotella and Faecalibacterium as well as Bifidobacterium of human gut microbiota.

Microbiome modulation after severe acute kidney injury accelerates functional recovery and decreases kidney fibrosis.

Targeting gut microbiota has shown promise to prevent experimental acute kidney injury (AKI). However, this has not been studied in relation to accelerating recovery and preventing fibrosis. Here, we found that modifying gut microbiota with an antibiotic administered after severe ischemic kidney injury in mice, particularly with amoxicillin, accelerated recovery. These indices of recovery included increased glomerular filtration rate, diminution of kidney fibrosis, and reduction of kidney profibrotic gene expression. Amoxicillin was found to increase stool Alistipes, Odoribacter and Stomatobaculum species while significantly depleting Holdemanella and Anaeroplasma. Specifically, amoxicillin treatment reduced kidney CD4+T cells, interleukin (IL)-17 +CD4+T cells, and tumor necrosis factor-α double negative T cells while it increased CD8+T cells and PD1+CD8+T cells. Amoxicillin also increased gut lamina propria CD4+T cells while decreasing CD8+T and IL-17+CD4+T cells. Amoxicillin did not accelerate repair in germ-free or CD8-deficient mice, demonstrating microbiome and CD8+T lymphocytes dependence for amoxicillin protective effects. However, amoxicillin remained effective in CD4-deficient mice. Fecal microbiota transplantation from amoxicillin-treated to germ-free mice reduced kidney fibrosis and increased Foxp3+CD8+T cells. Amoxicillin pre-treatment protected mice against kidney bilateral ischemia reperfusion injury but not cisplatin-induced AKI. Thus, modification of gut bacteria with amoxicillin after severe ischemic AKI is a promising novel therapeutic approach to accelerate recovery of kidney function and mitigate the progression of AKI to chronic kidney disease.