Gut Microbiota Community Research Articles

Xenobiotic metabolism activity of gut microbiota from six marine species: combined taxonomic, metagenomic, and in vitro transformation analysis

The xenobiotic metabolism driven by the gut microbiota significantly regulates the bioavailability and toxic effects of environmental pollutants such as plasticizers on aquatic organisms. However, it is still unknown whether the gut microbiota can exhibit variable metabolic ability across host species and which functional bacteria and genes are involved in xenobiotic transformation. This study investigated the enriched gut microbiota community composition and diversity of in vitro enrichment cultures from 6 marine species, namely, yellowfin seabream (Acanthopagrus latus), thorn fish (Terapon jarbua), shortnose ponyfish (Leiognathus brevirostris), mussel (Perna viridis), prawn (Parapenaeopsis hungerfordi) and crab (Charybdis riversandersoni). Pseudomonadota, Bacteroidota and Bacillota were the dominant phyla and Enterobacter, Raoultella, Klebsiella, Dysgonomanas and Lactococcus were the dominant genera in the enriched flora according to 16S rRNA sequencing. Furthermore, the metagenomic results revealed that all enriched gut microbiota presented metabolic genes for carbohydrates, amino acids, lipids, and xenobiotics. In particular, the gut microbiota of yellowfin seabream had the highest abundance of glycoside hydrolase family genes and CYP450 enzyme genes. Klebsiella was identified as a common potential degrader of xenobiotic metabolism. In addition, the Biolog plate test system confirmed that the gut microbiota can metabolize various carbon sources and drive the xenobiotic transformation. According to AWCD analysis of community level physiological profiling (CLPP), yellowfin seabream >mussel >prawn >shortnose ponyfish >crab >thorn fish. The gut microbiota of yellowfin seabream presented a stronger metabolic profile of phthalates and bisphenol analogs which reflected by their AWCD results and concentration variations. Overall, our results demonstrated the diverse metabolic abilities of the gut microbiota from six marine organisms and their potential for altering of the fate of xenobiotics in the ecosystem on the basis of combined taxonomic, metagenomic, and in vitro transformation analysis.

Lactobacillus rhamnosus RL-H3-005 and Pediococcus acidilactici RP-H3-006 ameliorate atopic dermatitis in offspring mice by modulating the gut microbiota

The increasing incidence of atopic dermatitis (AD) presents a public health issue, and thus there is an urgent need for safe and effective preventive strategies. In this study, a strategy to reduce the risk of AD in offspring by administering probiotics to the mother was explored. Female mice were given Lactobacillus rhamnosus RL-H3-005 (RL) and Pediococcus acidilactici RP-H3-006 (RP) during pregnancy and lactation period, and their inhibition effects on AD symptoms in offspring mice were evaluated. The results showed that supplementation with RL and RP during pregnancy and lactation period altered not only the gut microbiota community but also microbial community in milk in pregnant mice. Further study showed that pups from RL- and RP-treated pregnant mice had mild symptoms of AD, characterized by reduced epidermal thickness in the ear tissues and numbers of mast cells, which was associated with the reduction in secretory immunoglobulin A (sIgA), immunoglobulin E (IgE), IL-4, IL-5, IL-13, thymic stromal lymphopoietin (TSLP), and eosinophil cationic protein (Ecp). The underlying mechanism of RL and RP on the inhibition of AD symptom in offspring was closely associated with the alterations of the gut microbiota community in offspring, including an increase in Ligilactobacillus and Bacteroides. This study implies that RL and RP hold the potential to reduce the risk of AD in offspring via gut-mammary axis during the pregnancy and lactation period.

The role of early life factors and green living environment in the development of gut microbiota in infancy: Population-based cohort study

ObjectiveEarly life microbial exposure influences the composition of gut microbiota. We investigated how early life factors, and the green living environment around infants’ homes, influence the development of gut microbiota during infancy by utilizing data from the Steps to Healthy Development follow-up study (the STEPS study). MethodsThe gut microbiota was analyzed at early (∼3 months, n = 959), and late infancy (∼13 months, n = 984) using 16S rRNA amplicon sequencing, and combined with residential green environment, measured as (1) Normalized Difference Vegetation Index, (2) Vegetation Cover Diversity, and (3) Naturalness Index within a 750 m radius. We compared gut microbiota diversity and composition between early and late infancy, identified significant individual and family level early life factors influencing gut microbiota, and determined the role of the residential green environment measures on gut microbiota development. ResultsAlpha diversity (t-test, p < 0.001) and beta diversity (PERMANOVA, R2 = 0.095, p < 0.001) differed between early and late infancy. Birth mode was the strongest contributor to the gut microbiota community composition in early infancy (PERMANOVA, R2 = 0.005, p < 0.01) and the presence of siblings in late infancy (PERMANOVA, R2 = 0.007, p < 0.01). Residential green environment showed no association with community composition, whereas time spend outdoors did (PERMANOVA, R2 = 0.002, p < 0.05). Measures of greenness displayed a statistically significant association with alpha diversity during early infancy, not during late infancy (glm, p < 0.05). In adjusted analysis, the associations remained only with the Naturalness Index, where higher human impact on living environment was associated with decreased species richness (glm, Observed richness, p < 0.05). ConclusionsThe role of the residential green environment to the infant gut microbiota is especially important in early infancy, however, other early life factors, such as birth mode and presence of sibling, had a more significant effect on the overall community composition.

Mangiferin ameliorates polycystic ovary syndrome in rats by modulating insulin resistance, gut microbiota, and ovarian cell apoptosis.

Polycystic ovary syndrome (PCOS) is a complex endocrine and metabolic disorder characterized by hyperandrogenism, prolonged anovulation and polycystic ovaries. However, there are no effective interventions to treat this disorder. As previously shown, mangiferin modulated the AMPK and NLRP3 signal pathways to alleviate nonalcoholic fatty liver disease (NAFLD). In recent years, mangiferin has emerged as a promising drug candidate for treating metabolic diseases. In this study, we evaluated the effects of mangiferin on a letrozole (LET) combined with high-fat diet (HFD)-induced PCOS rat model through estrous cycle detection, serum/tissue biochemical analysis, and hematoxylin and eosin (HE) staining of ovarian tissue. The mechanisms of mangiferin's effects on PCOS rats were analyzed using 16S rRNA sequencing, RNA-seq, western blotting (WB), and immunohistochemical (IHC) staining. Our results displayed that mangiferin showed a promising effect in PCOS rats. It improved lipid metabolism, glucose tolerance, insulin resistance, hormonal imbalance, ovarian dysfunction, and adipocyte abnormalities. RNA-seq analysis indicated that mangiferin may be involved in several signal pathways, including apoptosis, necrosis, and inflammation. Furthermore, western blot and immunohistochemical staining demonstrated that mangiferin regulates Caspase-3 and Cytc, exhibiting anti-apoptotic activity in the ovaries. Additionally, mangiferin significantly altered the gut microbiota community of PCOS rats, changing the abundance of firmicutes, bacteroidota, proteobacteria, and actinobacteria at the phylum level and the abundance of Blautia, Coprococcus, Roseburia, and Pseudomonas at the genus level. In conclusion, mangiferin is a promising and novel therapeutic agent for PCOS as it ameliorates insulin resistance, gut microbiota and ovarian cell apoptosis.

Multi-omics joint analysis reveals that the Miao medicine Yindanxinnaotong formula attenuates non-alcoholic fatty liver disease

BackgroudNon-alcoholic fatty liver disease (NAFLD) is a growing chronic liver disease worldwide, and no effective agent is approved yet for this condition. Traditional Chinese Medicine (TCM), which has been practiced for thousands of years in China and other Asian countries, is considered an important source for identifying novel medicines for various diseases. Miao medicine Yindanxinnaotong formula (YDX) is a classical TCM for the treatment of hyperlipidemia disease by reducing blood lipid content, while the role of YDX have not been clarified in NAFLD. PurposeTo investigate the protective effect of YDX on NAFLD in mice induced by high fat diet (HFD) and clarify the potential mechanism. MethodsNAFLD mice model was constructed by receiving HFD for 10-week period with or without YDX administration. Lipid profiles, biochemical indicators, and histopathological staining were performed to evaluate the extent of hepatic lipid accumulation and hepatic steatosis. 16S rRNA sequencing was used to determine the gut microbial composition. Serum metabolomics was further used to investigate the changes in plasma biomarkers for NAFLD-associated by UPLC-Q-TOF/MS analysis. Subsequently, liver transcriptomics was employed to identify differentially expressed genes and explore regulatory pathways. Then, lipid metabolism–related proteins and inflammation factors were examined by Western blot and ELISA. ResultsYDX reduced body weight gain, liver index and inflammatory cytokines levels, along with improved hepatic steatosis, serum lipid profile, sensitivity to insulin and also tolerance to glucose, and enhanced oxidative defense system in HFD-induced mice. Also, YDX remarkedly affected gut microbiota diversity and community richness and decreased the ratio of Firmicutes/Bacteroidetes. Meanwhile, YDX also reduced the production of harmful lipid metabolites in the sera of NAFLD mice, such as LPC(18:0), LPC(18:1) and carnitine. Notably, consistent with liver transcriptomics results, YDX downregulated the expression of proteins implicated in de novo lipid synthesis (Srebp-1c, Acaca, Fasn, Scd-1, and Cd36) and pro-inflammatory cytokines (IL-6 and TNF-α), and increased the expression of proteins-related fatty acid β-oxidation (Ampkα, Ppar-α, and Cpt-1) in the liver by activating Ampk pathway. ConclusionYDX is promisingly an effective therapy for preventing NAFLD by modulating the Ampk pathway, inhibiting gut microbiota disorder, and reducing the production of harmful lipid metabolites.

Associations between gut microbiota and osteoporosis or osteopenia in a cohort of Chinese Han youth

Osteoporosis (OP) is a common metabolic bone disease characterized by low bone mass and microstructural deterioration of bone. Changes in the composition and structure of gut microbiota (GM) are related to changes of bone mass and bone microstructure. However, the relationship between GM and bone mineral density (BMD) is complex, and data are especially scarce for Chinese Han youth. Therefore, 62 Chinese Han youth participants were recruited. Furthermore, according to the T–score evaluation criteria of the World Health Organization (WHO), we divided the BMD levels of participants into three groups: osteoporosis\\BDL, osteopenia\\BDM, normal bone density\\BDH, and the associations between GM community and BMD groups were conducted. According to alpha and beta diversity analysis, significant differences were found in the microbial richness and composition between groups. The dominant phyla of GM in a cohort of Chinese Han youth were Bacteroidota (50.6%) and Firmicutes (41.6%). Anaerobic microorganisms, such as g_Faecalibacterium and g_Megamonas, account for the largest proportion in the gut, which were mainly Firmicutes phylum. The dominant genera and species in the three BMD groups were g_Prevotella, g_Bacteroides, g_Faecalibacterium, g_Megamonas, s_Prevotella copri, s_unclassified_g_Faecalibacterium, s_unclassified_g_Prevotella, s_unclassified_g_Bacteroides and s_Bacteroides plebeius. g_Faecalibacterium, g_Bacteroides and g_Ruminococcus differed between the BDH and BDL groups as well as between the BDH and BDM groups. LEfSe showed three genus communities and eight species communities were enriched in the three BMD groups, respectively. The associations between microbial relative abundance and T–score was not statistically significant by Spearman and regression analysis. In conclusion, the alpha diversity indexes in the BDH group were higher than in the BDL group, and several taxa were identified that may be the targets for diagnosis and therapy of OP.

Comparison of the Intestinal Microbiota Composition and Function of Red Claw Crayfish (Cherax quadricarinatus) Cultured in Ponds and Rice Fields

The growth environment significantly influences the intestinal microbiota of aquatic organisms. We investigated the composition and functional differences in the intestinal microbiota of red claw crayfish (Cherax quadricarinatus) in rice fields (RB) and ponds (PB) by 16S rDNA high-throughput sequencing technology. The results indicate that the Shannon, Simpson, Sobs, Chao1, and ACE indices of PB are all higher than those of RB, demonstrating greater diversity and richness of intestinal microbiota. The dominant phyla in the intestinal microbiota of the Cherax quadricarinatus were Proteobacteria, Tenericutes, and Firmicutes. Tenericutes and Proteobacteria were significantly more abundant in the RB than in the PB, while Planctomycetes and Firmicutes were significantly more abundant in the PB than in the RB. The results of network correlation analysis indicate that Proteobacteria and Firmicutes exhibit strong connectivity with other microbial groups in the gut microbiota of Cherax quadricarinatus, showing significant centrality. They play an important role in the interactions within the gut microbiota community. The dominant bacterial genera in the Cherax quadricarinatus’s gut were Citrobacter, Candidatus_Bacilloplasma, and Clostridium_sensu_stricto_1. The abundance of the genus Clostridium was significantly higher in the PB than in the RB, whereas the abundance of Candidatus_Hepatoplasma and Vibrio was significantly lower in the PB than in the RB. The prediction function of KEGG enrichment showed that the abundance of Amino acid metabolism, Biosynthesis of Other Secondary Metabolites, Transport and Catabolism, Cancers, and Nervous System, Substance Dependence were significantly higher in the PB, while the infectious diseases pathway was enriched in the RB. In summary, our results revealed significant differences in the composition and diversity of intestinal microbiota in the Cherax quadricarinatus between rice paddy and pond farming environments. The intestinal microbiota of the Cherax quadricarinatus grown in pond environments exhibit higher diversity and stability, manifested by an increase in beneficial bacteria abundance and a decrease in opportunistic pathogens. These findings significantly improve understanding of the complex relationship among Cherax quadricarinatus, intestinal microbiota, and the environment.

Impacts of industrial food wastes on nutritional value of mealworm (Tenebrio molitor) and its gut microbiota community shift

The extensive investigation into the capacity of mealworms to digest diverse food by-products, as well as plastic wastes, has been a focal point in recent years. The transition from traditional diet sources like brans to food wastes has the potential to impact the physiological properties of mealworms. This study explored the utilization of various industrial food wastes such as okara, barley spent grain (BSG), sesame oil meal (SOM), and spent coffee grounds (SCG) as feed alternatives, and reports on their survival rate, biomass variations, and nutritional composition. In additional, the shift in their gut microbiota was also assessed. Among the range of industrial food wastes, mealworms exhibited the most robust growth performance when nourished with BSG. This particular group showed a survival rate of 98.33 % and a biomass increase of 23.06 %. In contrast, mealworms fed with SCG demonstrated the lowest survival rate and experienced a significant reduction in biomass. Although the groups fed with okara and SCG displayed moderate growth performance, both exhibited protein levels comparable to those observed in the oatmeal-fed group (used as the positive control). Notably, the inclusion of BSG in the mealworm diet exhibited the potential to enrich their omega-3 fatty acid content, suggesting potential benefits for applications as animal feed or even human consumption. Furthermore, an analysis of the gut microbiome was conducted to investigate the associations between specific diets and the composition of mealworm gut microbiota. In summary, food wastes such as BSG may be repurposed as feed substrates for mealworms before converting them into an alternative source of protein.

Potassium-induced κ-carrageenan helices resist degradation by gut microbiota in an in vitro model

Higher-order structures hierarchy of κ-carrageenan in the presence of potassium was reported. Yet, the destiny of κ-carrageenan in higher-order structures in the colon and their impacts on the gut microbiota community remains to be revealed. This study aims to investigate the fermentation behaviors and trace the structural change of higher-order structures of κ-carrageenan during in vitro fermentation. Herein, κ-carrageenan gels were induced in the presence of 10, 40, and 70 mmol/L potassium ions, and a structural-hierarchical transition from secondary to quaternary structures was observed using an AFM and TEM. Results from GPC-MALLS, TLC, IEC, and GC indicated that Single helices were partially fermented by fecal microbiota, while supercoiled helices (tertiary structures) and intertwined helices networks (quaternary structures) were hardly fermented. Tracing the structural change of higher-order κ-carrageenan suggested that the single helices were partially deformed, as shown by the 60% reduction of single helices width, while supercoiled helices were more resistant to fermentation compared to single helices. The super-strands networks were hardly fermented as their width distribution center had been sustained at around 90 nm from 12 to 48 h. In addition, the 16S rRNA gene (V3-V4) amplicon sequencing results indicated that Bifidobacterium longum showed a positive correlation to the structural hierarchy (R = 0.734, p < 0.01). Together, the higher-order structures hierarchy of κ-carrageenan can resist degradation by human gut microbiota.

Dysbiosis of the gut microbiota in glioblastoma patients and potential biomarkers for risk assessment

BackgroundThe significant death rate of glioblastoma is well-known around the world. The link between gut microbiota and glioma is becoming more studied. The goal of this study was to look at the relationships between intestinal flora and glioblastoma, and to provide a new perspective for the diagnosis as well as treatment of glioblastoma. MethodsFecal samples from 80 participants with glioblastoma (n = 40) and healthy individuals (n = 40) in this study were collected as well as analyzed utilizing 16S rRNA gene amplicon sequencing in order to characterize the gut microbial community. ResultsEach group has its own microbial community, and the microbial environment of glioblastoma patients had lower richness and evenness. The structure of gut microbiota community in glioblastoma patients showed profound changes, which includes the increase of pathogens in Fusobacteria and Bacteroidetes, and the reduction of probiotic bacteria in Firmicutes, Actinobacteria and Verrucomicrobia. Meanwhile, the significant correlations and clustering of OTUS (operational taxonomic units) in glioblastoma patients were discovered, and a biomarker panel (Fusobacterium, Escherichia/Shigella, Ruminococcus gnavus group, Lachnospira, Akkermansia, Parasutterella) had been used to discriminate the patients with glioblastoma from the healthy subjects (AUC: 0.80). Furthermore, the glioblastoma group exhibited multiple disturbed pathways through KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis, particularly in genetic information processing. Moreover, the prediction of phenotypic characteristics of microbiome proposed that the glioblastoma patients might have more Gram-negative bacteria and opportunistic pathogens than the healthy controls. ConclusionsWhen compared to healthy people, glioblastoma sufferers have a different host-microbe interaction. Furthermore, certain types of intestinal flora could be regarded as biomarkers and drug targets for the diagnosis as well as treatment of glioblastomas.

Alterations in the gut microbiota community are associated with childhood obesity and precocious puberty

ObjectiveTo explore the distribution and differences in the intestinal microbiota in girls with obesity-related precocious puberty and the relationship between intestinal microbiota and obesity-related precocious puberty.Methods16 S rRNA gene amplicons from fecal samples from girls with precocious puberty and obesity-complicated precocious puberty and healthy children were sequenced to define microbial taxa.ResultsThe α- and β-diversity indices of the microbiome significantly differed among the three groups. At the phylum level, the proportions of Firmicutes, Actinobacteriota, Bacteroidota, Bacteria, Campylobacterota, and Acidobacteriota were different. At the genus level, there were differences in Bifidobacterium, Bacteroides, Anaerostipes, Fusicatenibacter, Klebsiella, Lachnospiraceae, ErysipelotrichaceaeUCG-003, Prevotella9, Ruminococcus gnavus group, and Lachnoclostridium. Additionally, Bifidobacterium, Anaerostipes, Bacteroides, Candidatus Microthrix, Eubacterium hallii group, Klebsiella, and Erysipelotrichaceae UCG-003 were identified as bacterial biomarkers by LEfSe. Furthermore, Sellimonas, Intestinibacter, Anaerostipes, Ruminococcus gnavus group, and Oscillibacter were identified as the differential biomarkers by random forest. A receiver operating characteristic (ROC) curve was used to evaluate the biomarkers with high predictive value for obesity-related precocious puberty. Spearman correlation analysis confirmed that Anaerostipes levels were negatively correlated with body weight, body mass index (BMI), bone age, luteinizing hormone, follicle-stimulating hormone, and estradiol.ConclusionsThere was a significant correlation between obesity-associated precocious puberty and gut microbiota, especially the functional characteristics of the microbiome and its interactions, which can provide a theoretical basis for the clinical intervention of obesity and precocious puberty through the microbiome.

Changes in bumblebee queen gut microbiotas during and after overwintering diapause.

Bumblebees are key pollinators with gut microbiotas that support host health. After bumblebee queens undergo winter diapause, which occurs before spring colony establishment, their gut microbiotas are disturbed, but little is known about community dynamics during diapause itself. Queen gut microbiotas also help seed worker microbiotas, so it is important that they recover post-diapause to a typical community structure, a process that may be impeded by pesticide exposure. We examined how bumblebee queen gut microbiota community structure and metabolic potential shift during and after winter diapause, and whether post-diapause recovery is affected by pesticide exposure. To do so, we placed commercial Bombus impatiens queens into diapause, euthanizing them at 0, 2 and 4 months of diapause. Additionally, we allowed some queens to recover from diapause for 1 week before euthanasia, exposing half to the common herbicide glyphosate. Using whole-community, shotgun metagenomic sequencing, we found that core bee gut phylotypes dominated queen gut microbiotas before, during and after diapause, but that two phylotypes, Schmidhempelia and Snodgrassella, ceased to be detected during late diapause and recovery. Despite fluctuations in taxonomic community structure, metabolic potential remained constant through diapause and recovery. Also, glyphosate exposure did not affect post-diapause microbiota recovery. However, metagenomic assembly quality and our ability to detect microbial taxa and metabolic pathways declined alongside microbial abundance, which was substantially reduced during diapause. Our study offers new insights into how bumblebee queen gut microbiotas change taxonomically and functionally during a key life stage and provides guidance for future microbiota studies in diapausing bumblebees.

Dietary vitamin B6 supplementation alleviates heat stress-induced intestinal barrier impairment by regulating the gut microbiota and metabolites in broilers

Heat stress (HS) brings great challenges to the poultry industry. Vitamin B6 (VB6) is an essential micro-nutrient for animals to maintain normal physiological functions and possesses antioxidant and anti-inflammatory properties. This study aimed to explore the effect of VB6 on alleviating HS-induced intestinal barrier impairment in broilers. A total of 250 broilers (609.76 ± 0.34 g) were randomly allocated to 5 groups with 5 replicate cages of 10 birds each. The broilers in thermoneutral (TN) group were raised in thermoneutral conditions (23 ± 1°C) and fed with a basal diet. The birds in other four groups were housed under cycle high temperature (34 ± 1°C for 8 h/d) from d 21 to 35 and fed with the basal diet (HS group) or basal diet supplemented with 6, 12, or 24 mg/kg VB6 (HB-6, HB-12, HB-24 groups). The results showed that HS reduced the growth performance, increased ileum inflammatory cytokines levels, and impaired the gut barrier function (P < 0.05). Compared to the HS group, final body weight, average daily gain, and average daily feed intake, and the feed conversion ratio were improved by VB6 supplementation. The diamine oxidase, interleukin (IL)-1β, tumor necrosis factor-α, IL-18, IL-10, and interferon-γ levels were reduced by VB6 supplementation (P < 0.05). Moreover, VB6 supplementation linearly or quadratically enhanced villus height and villus height-to-crypt depth ratio of duodenum and jejunum, and decreased crypt depth of duodenum and ileum. The mRNA expression of Occlaudin, ZO1, Mucin2, Mucin4, E-cadhein, and β-catenin were increased by VB6 treatment (P < 0.05). Furthermore, dietary VB6 altered the diversity and community of gut microbiota (P < 0.05). A total of 83 differential metabolites associated with the amelioration of VB6 were identified, which were primarily enriched in glycerophospholipid metabolism, caffeine metabolism, and glutathione metabolism pathway. Collectively, VB6 may improve the growth performance and intestinal barrier function of heat-stressed broilers by regulating the ileal microbiota and metabolic homeostasis.

High-fat intake induces gut microbiota disorders, inflammatory responses and oxidative stress in Nyctereutes procyonoides

The Nyctereutes procyonoides is highly regarded in the farming and leather industries because of the high value of its fur, which renders artificial feeding a crucial aspect. However, high-fat diets have always been associated with a variety of digestive disorders. This study aimed to investigate the impact of high-fat diets on the gut microbiota and the mechanisms of gut damage in Nyctereutes procyonoides. 16S rRNA sequencing demonstrated that high-fat diets caused diarrhea and intestinal damage through alterations in the gut microbiota: a decrease in the abundance of Firmicutes, an increase in the abundance of Proteobacteria and Actinobacteria, and an increase in the abundance of Enterococcaceae, Escherichia coli-Shigella, Clostridium and Lactobacillus. Subsequently, changes in metabolic pathways, such as amino and fatty acid pathways, were identified by KEGG and COG enrichment analysis, and the TLR4/NF-κB/NLRP3 inflammatory signaling pathway was shown to be activated by high-fat diets. In addition, high-fat diets lead to the accumulation of ROS and MDA and reduce the activity of the antioxidant enzymes GSH-PX and SOD. Correspondingly, the levels of proinflammatory cytokines (IL-6, IL-1β and TNF-α) were significantly increased, and the apoptosis and necrosis signaling pathways of colonic cells were detected, causing a dramatic decrease in the expression of intestinal tight junction proteins (Occludin, E-cadherin, ZO-1 and ZO-2). In conclusion, high-fat diets altered the structure of the Nyctereutes procyonoides gut microbiota community and led to colon damage. This study provides new insights into the intestinal health of Nyctereutes procyonoides.Graphical

Microplastics predominantly affect gut microbiota by altering community structure rather than richness and diversity: A meta-analysis of aquatic animals

The impacts of microplastics on the gut microbiota, a crucial component of the health of aquatic animals, remain inadequately understood. This phylogenetically controlled meta-analysis aims to identify general patterns of microplastic effects on the alpha diversity (richness and Shannon index), beta diversity, and community structure of gut microbiota in aquatic animals. Data from 63 peer-reviewed articles on the Web of Science were synthesized, encompassing 424 observations across 31 aquatic species. The analysis showed that microplastics significantly altered the community structure of gut microbiota, with between-group distances being 87.75% higher than within-group distances. This effect was significant even at environmentally relevant concentrations (≤1 mg L−1). However, their effects on richness, Shannon index, and beta diversity (community variation) were found to be insignificant. The study also indicated that the effects of microplastics were primarily dependent on their concentration and size, while the phylogeny of tested species explained limited heterogeneity. Furthermore, variations in gut microbiota alpha diversity, beta diversity, and community structure were correlated with changes in antioxidant enzyme activities from the liver and hepatopancreas. This implies that gut microbiota attributes of aquatic animals may provide insights into host antioxidant levels. In summary, this study illuminates the impacts of microplastics on the gut microbiota of aquatic animals and examines the implications of these effects for host health. It emphasizes that microplastics mainly alter the community structure of gut microbiota rather than significantly affecting richness and diversity.

Comparison between 16S rRNA and shotgun sequencing in colorectal cancer, advanced colorectal lesions, and healthy human gut microbiota

BackgroundGut dysbiosis has been associated with colorectal cancer (CRC), the third most prevalent cancer in the world. This study compares microbiota taxonomic and abundance results obtained by 16S rRNA gene sequencing (16S) and whole shotgun metagenomic sequencing to investigate their reliability for bacteria profiling. The experimental design included 156 human stool samples from healthy controls, advanced (high-risk) colorectal lesion patients (HRL), and CRC cases, with each sample sequenced using both 16S and shotgun methods. We thoroughly compared both sequencing technologies at the species, genus, and family annotation levels, the abundance differences in these taxa, sparsity, alpha and beta diversities, ability to train prediction models, and the similarity of the microbial signature derived from these models.ResultsAs expected, the results showed that 16S detects only part of the gut microbiota community revealed by shotgun, although some genera were only profiled by 16S. The 16S abundance data was sparser and exhibited lower alpha diversity. In lower taxonomic ranks, shotgun and 16S highly differed, partially due to a disagreement in reference databases. When considering only shared taxa, the abundance was positively correlated between the two strategies. We also found a moderate correlation between the shotgun and 16S alpha-diversity measures, as well as their PCoAs. Regarding the machine learning models, only some of the shotgun models showed some degree of predictive power in an independent test set, but we could not demonstrate a clear superiority of one technology over the other. Microbial signatures from both sequencing techniques revealed taxa previously associated with CRC development, e.g., Parvimonas micra.ConclusionsShotgun and 16S sequencing provide two different lenses to examine microbial communities. While we have demonstrated that they can unravel common patterns (including microbial signatures), shotgun often gives a more detailed snapshot than 16S, both in depth and breadth. Instead, 16S will tend to show only part of the picture, giving greater weight to dominant bacteria in a sample. Therefore, we recommend choosing one or another sequencing technique before launching a study. Specifically, shotgun sequencing is preferred for stool microbiome samples and in-depth analyses, while 16S is more suitable for tissue samples and studies with targeted aims.

Gut microbiota: a potential influencer of insomnia occurring after COVID-19 infection.

The prevalence of insomnia has increased in recent years, significantly affecting the lives of many individuals. Coronavirus disease 2019 (COVID-19) infection has been found to have a substantial impact on the human gut microbiota (GM). Clinical studies have shown that the high prevalence, prolonged duration, and refractory treatment of insomnia symptoms following the COVID-19 pandemic may be related to the effect of COVID-19 infection on the GM. Therefore, the GM may be a potential target for the treatment of insomnia following COVID-19 infection. However, relevant studies have not been well-documented, and the GM has not been sufficiently analyzed in the context of insomnia treatment. Herein, we review the interaction between sleep and the GM, summarize the characteristics of COVID-19-induced abnormal changes in the GM and metabolites in patients with insomnia, and discuss potential mechanisms, including metabolic, immune, and neural pathways, by which these abnormal changes in the GM cause insomnia as well as the factors affecting the GM. Finally, we discuss the prospect of modulating the host GM community for the effective treatment of insomnia after COVID-19 infection and the need for further clinical studies.

A history of repeated antibiotic usage leads to microbiota-dependent mucus defects

ABSTRACT Recent evidence indicates that repeated antibiotic usage lowers microbial diversity and ultimately changes the gut microbiota community. However, the physiological effects of repeated – but not recent – antibiotic usage on microbiota-mediated mucosal barrier function are largely unknown. By selecting human individuals from the deeply phenotyped Estonian Microbiome Cohort (EstMB), we here utilized human-to-mouse fecal microbiota transplantation to explore long-term impacts of repeated antibiotic use on intestinal mucus function. While a healthy mucus layer protects the intestinal epithelium against infection and inflammation, using ex vivo mucus function analyses of viable colonic tissue explants, we show that microbiota from humans with a history of repeated antibiotic use causes reduced mucus growth rate and increased mucus penetrability compared to healthy controls in the transplanted mice. Moreover, shotgun metagenomic sequencing identified a significantly altered microbiota composition in the antibiotic-shaped microbial community, with known mucus-utilizing bacteria, including Akkermansia muciniphila and Bacteroides fragilis, dominating in the gut. The altered microbiota composition was further characterized by a distinct metabolite profile, which may be caused by differential mucus degradation capacity. Consequently, our proof-of-concept study suggests that long-term antibiotic use in humans can result in an altered microbial community that has reduced capacity to maintain proper mucus function in the gut.

Genetic hypogonadal (Gnrh1hpg) mouse model uncovers influence of reproductive axis on maturation of the gut microbiome during puberty.

The gut microbiome plays a key role in human health and gut dysbiosis is linked to many sex-specific diseases including autoimmune, metabolic, and neurological disorders. Activation of the hypothalamic-pituitary-gonadal (HPG) axis during puberty leads to sexual maturation and development of sex differences through the action of gonadal sex steroids. While the gut microbiome also undergoes sex differentiation, the mechanisms involved remain poorly understood. Using a genetic hypogonadal (hpg) mouse model, we sampled the fecal microbiome of male and female wild-type and hpg mutant mice before and after puberty to determine how microbial taxonomy and function are influenced by age, sex, and the HPG axis. We showed that HPG axis activation during puberty is required for sexual maturation of the gut microbiota composition, community structure, and metabolic functions. We also demonstrated that some sex differences in taxonomic composition and amine metabolism developed independently of the HPG axis, indicating that sex chromosomes are sufficient for certain sex differences in the gut microbiome. In addition, we showed that age, independent of HPG axis activation, led to some aspects of pubertal maturation of the gut microbiota community composition and putative functions. These results have implications for microbiome-based treatments, indicating that sex, hormonal status, and age should be considered when designing microbiome-based therapeutics.

The Association of Neonatal Gut Microbiota Community State Types with Birth Weight.

while most gut microbiota research has focused on term infants, the health outcomes of preterm infants are equally important. Very-low-birth-weight (VLBW) or extremely-low-birth-weight (ELBW) preterm infants have a unique gut microbiota structure, and probiotics have been reported to somewhat accelerate the maturation of the gut microbiota and reduce intestinal inflammation in very-low preterm infants, thereby improving their long-term outcomes. The aim of this study was to investigate the structure of gut microbiota in ELBW neonates to facilitate the early identification of different types of low-birth-weight (LBW) preterm infants. a total of 98 fecal samples from 39 low-birth-weight preterm infants were included in this study. Three groups were categorized according to different birth weights: ELBW (n = 39), VLBW (n = 39), and LBW (n = 20). The gut microbiota structure of neonates was obtained by 16S rRNA gene sequencing, and microbiome analysis was conducted. The community state type (CST) of the microbiota was predicted, and correlation analysis was conducted with clinical indicators. Differences in the gut microbiota composition among ELBW, VLBW, and LBW were compared. The value of gut microbiota composition in the diagnosis of extremely low birth weight was assessed via a random forest-machine learning approach. we briefly analyzed the structure of the gut microbiota of preterm infants with low birth weight and found that the ELBW, VLBW, and LBW groups exhibited gut microbiota with heterogeneous compositions. Low-birth-weight preterm infants showed five CSTs dominated by Enterococcus, Staphylococcus, Klebsiella, Streptococcus, Pseudescherichia, and Acinetobacter. The birth weight and clinical indicators related to prematurity were associated with the CST. We found the composition of the gut microbiota was specific to the different types of low-birth-weight premature infants, namely, ELBW, VLBW, and LBW. The ELBW group exhibited significantly more of the potentially harmful intestinal bacteria Acinetobacter relative to the VLBW and LBW groups, as well as a significantly lower abundance of the intestinal probiotic Bifidobacterium. Based on the gut microbiota's composition and its correlation with low weight, we constructed random forest model classifiers to distinguish ELBW and VLBW/LBW infants. The area under the curve of the classifiers constructed with Enterococcus, Klebsiella, and Acinetobacter was found to reach 0.836 by machine learning evaluation, suggesting that gut microbiota composition may be a potential biomarker for ELBW preterm infants. the gut bacteria of preterm infants showed a CST with Enterococcus, Klebsiella, and Acinetobacter as the dominant genera. ELBW preterm infants exhibit an increase in the abundance of potentially harmful bacteria in the gut and a decrease in beneficial bacteria. These potentially harmful bacteria may be potential biomarkers for ELBW preterm infants.