Mucosal Microbiota Research Articles

Host innate and adaptive immunity shapes the gut microbiota biogeography.

The gut microbiota has a fundamental role in the development and the maturation of the host immune system. Both innate and adaptive immune cells have critical functions in microbial pathogen containment and clearance, but the regulation of the commensal microbiome ecosystem in the gastrointestinal tract by these major immune cell populations is incompletely defined. The role of specific innate and adaptive immune cell in the regulation of the microbiota in the intestinal tract biogeographically was investigated. Dendritic cells, macrophages, CD4+ T-cells, CD8+ T-cells, and B-cells were depleted using monoclonal antibodies and clodronate liposomes, and the microbial communities were determined by 16S rRNA gene sequencing. With specific immune cell depletion, distinct microbiota changes were observed. In general, immune cell depleted mice had higher microbiota richness and evenness at all gut anatomical sites. At each gut segment, samples from immune cell-depleted animals clustered away from the isotype/liposome control mice. This was especially dramatic for the small intestinal microbiota. Specifically, Enterobacteriaceae, Bacteroides acidifaciens, and Mucispirillum schaedleri were highly enriched in the mucosa and lumen of the small intestine in immune cell-deficient animals. Further, the mucosal microbiota had higher microbiota evenness compared with luminal microbiota at all gut segments, and the UniFrac distance between B cell depleted and isotype control mice was the largest in the duodenum followed by the ileum and colon. Taken together, the data suggest that innate and adaptive immune cells specifically contribute to the regulation of the gut microbiota's biogeographical distribution along the gastrointestinal tract, and microbiota in the duodenum mucosa are more responsive to host immune changes compared with other anatomical sites.

Delay of Feed Post-Hatch Causes Changes in Expression of Immune-Related Genes and Their Correlation with Components of Gut Microbiota, but Does Not Affect Protein Expression

Simple SummaryNewly hatched chicks do not have access to feed until between 48 and 72 h post-hatch based on standard practices in the poultry industry. How these practices affect the chicken’s immune system in not well understood. In this study, we investigated the effect of a delay in access to feed for 48 h in newly hatched chicks on the expression of various immune-related genes in the ileum and analyzed the correlation between these genes and the components of the ileal microbiota. The results suggest that several immune-related genes were affected by delayed access to feed and the age of the birds; however, these changes were transient, occurring mostly within 48 h of the return of birds to feed. In the correlation analysis between gene expression and components of the ileal microbiota, an increased number of significant correlations between immune-related genes and the genera Clostridium, Enterococcus, and the species Clostridium perfringens suggests a perturbation of the immune response and ileal microbiota in response to lack of feed immediately post-hatch. These results point out the complexity of the interplay between microbiota and the immune response and will help further explain the negative effects of delay in access to feed on production parameters in chickens.Because the delay of feed post-hatch (PH) has been associated with negative growth parameters, the aim of the current study was to determine the effect of delayed access to feed in broiler chicks on the expression of immune-related genes and select proteins. In addition, an analysis of the correlation between gene expression and components of the gut microbiota was carried out. Ross 708 eggs were incubated and hatched, and hatchlings were divided into FED and NONFED groups. The NONFED birds did not have access to feed until 48 h PH, while FED birds were given feed immediately PH. The ileum from both groups (n = 6 per group) was sampled at embryonic day 19 (e19) and day 0 (wet chicks), and 4, 24, 48, 72, 96, 144, 192, 240, 288, and 336 h PH. Quantitative PCR (qPCR) was carried out to measure the expression of avian interleukin (IL)-1β, IL-4, IL-6, IL-8, IL-18, transforming growth factor (TGF-β), toll-like receptor (TLR)2, TLR4, interferon (IFN)-β, IFN-γ, and avian β-defensins (AvBD) I, 2, 3, 5, 6, 7, 8, 9, and 10. Protein expression of IL-10, IL-1β, IL-8, and IL-18 were measured using ELISAs. A correlation analysis was carried out to determine whether any significant association existed between immune gene expression and components of the ileal luminal and mucosal microbiota. Expression of several immune-related genes (TGF-β, TLR4, IFN-γ, IL-1β, IL-4, IL-6, and AvBDs 8 and 9) were significantly affected by the interaction between feed status and age. The effects were transient and occurred between 48 and 96 h PH. The rest of the genes and four proteins were significantly affected by age, with a decrease in expression noted over time. Correlation analysis indicated that stronger correlations exist among gene expression and microbiota in NONFED birds. The data presented here indicates that delay in feed PH can affect genes encoding components of the immune system. Additionally, the correlation analysis between immune gene expression and microbiota components indicates that a delay in feed has a significant effect on the interaction between the immune system and the microbiota.

Neisseria genes required for persistence identified via in vivo screening of a transposon mutant library.

The mechanisms used by human adapted commensal Neisseria to shape and maintain a niche in their host are poorly defined. These organisms are common members of the mucosal microbiota and share many putative host interaction factors with Neisseria meningitidis and Neisseria gonorrhoeae. Evaluating the role of these shared factors during host carriage may provide insight into bacterial mechanisms driving both commensalism and asymptomatic infection across the genus. We identified host interaction factors required for niche development and maintenance through in vivo screening of a transposon mutant library of Neisseria musculi, a commensal of wild-caught mice which persistently and asymptomatically colonizes the oral cavity and gut of CAST/EiJ and A/J mice. Approximately 500 candidate genes involved in long-term host interaction were identified. These included homologs of putative N. meningitidis and N. gonorrhoeae virulence factors which have been shown to modulate host interactions in vitro. Importantly, many candidate genes have no assigned function, illustrating how much remains to be learned about Neisseria persistence. Many genes of unknown function are conserved in human adapted Neisseria species; they are likely to provide a gateway for understanding the mechanisms allowing pathogenic and commensal Neisseria to establish and maintain a niche in their natural hosts. Validation of a subset of candidate genes confirmed a role for a polysaccharide capsule in N. musculi persistence but not colonization. Our findings highlight the potential utility of the Neisseria musculi-mouse model as a tool for studying the pathogenic Neisseria; our work represents a first step towards the identification of novel host interaction factors conserved across the genus.

Royal Jelly Protected against Dextran-Sulfate-Sodium-Induced Colitis by Improving the Colonic Mucosal Barrier and Gut Microbiota.

Royal jelly (RJ) is a natural bee product that contains a variety of biologically active ingredients and has antitumor, antiallergic, antibacterial and immune-regulating effects. Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the intestine that can cause abdominal pain and diarrhea. With this study, we aimed to explore the protective effect of RJ on DSS-induced colitis in mice. The physiochemical parameters (water, protein, 10-hydroxy-2-decenoic acid, total sugar, starch, ash and acidity) of the RJ samples used in this study met the requirements of the international and Chinese national standards. Treatment with RJ improved symptoms and colonic cell apoptosis and decreased intestinal permeability by increasing the expression of tight-junction protein, goblet cells and their secretion mucin, MUC2, in DSS-induced ulcerative colitis mice. RJ also reduced the expression of proinflammatory cytokine IL-6 and increased the expression of anti-inflammatory cytokine IL-10 and sIgA. DSS resulted in an increase in the relative abundance of Parabacteroides, Erysipelotrichaceae, Proteobacteria (Gammaproteobacteria, Enterobacteriales and Enterobacteriaceae) and Escherichia Shigella in the colon and a decrease in the relative abundance of Muribaculum. In the RJ treatment group, the relative abundance of the above intestinal flora was improved by treatment with 2.0 g/kg RJ. These results suggested that RJ alleviated DSS-induced colitis by improving the colonic mucosal barrier.

Fusobacterium nucleatum promotes colon cancer progression by changing the mucosal microbiota and colon transcriptome in a mouse model.

BACKGROUND Fusobacterium nucleatum (F. nucleatum) has long been known to cause opportunistic infections and has recently been implicated in colorectal cancer (CRC), which has attracted broad attention. However, the mechanism by which it is involved in CRC development is not fully understood.AIMTo explore its potential causative role in CRC development, we evaluated the colon pathology, mucosa barrier, colon microbiota and host transcriptome profile after F. nucleatum infection in an azoxymethane/dextran sulfate sodium salt (AOM/DSS) mouse model.METHODSThree groups of mice were compared to reveal the differences, i.e., the control, AOM/DSS-induced CRC and AOM/DSS-FUSO infection groups.RESULTSBoth the AOM/DSS and AOM/DSS-FUSO groups exhibited a significantly reduced body weight and increased tumor numbers than the control group, and AOM/DSS mice with F. nucleatum infection showed the highest tumor formation ratio among the three groups. Moreover, the colon pathology was the most serious in the AOM/DSS-FUSO group. We found that the structure of the colon microbiota changed considerably after F. nucleatum infection; striking differences in mucosal microbial population patterns were observed between the AOM/DSS-FUSO and AOM/DSS groups, and inflammation-inducing bacteria were enriched in the mucosal microbiota in the AOM/DSS-FUSO group. By comparing intestinal transcriptomics data from AOM vs AOM/DSS-FUSO mice, we showed that transcriptional activity was strongly affected by dysbiosis of the gut microbiota. The most microbiota-sensitive genes were oncogenes in the intestine, and the cyclic adenosine monophosphate signaling pathway, neuroactive ligand–receptor interaction, PPAR signaling pathway, retinol metabolism, mineral absorption and drug metabolism were highly enriched in the AOM/DSS-FUSO group. Additionally, we showed that microbial dysbiosis driven by F. nucleatum infection enriched eight taxa belonging to Proteobacteria, which correlates with increased expression of oncogenic genes.CONCLUSIONOur study demonstrated that F. nucleatum infection altered the colon mucosal microbiota by enriching pathogens related to the development of CRC, providing new insights into the role of F. nucleatum in the oncogenic microbial environment of the colon.

Gut mucosal microbiota profiles linked to colorectal cancer recurrence.

BACKGROUNDEmerging evidence links gut microbiota to various human diseases including colorectal cancer (CRC) initiation and development. However, gut microbiota profiles associated with CRC recurrence and patient prognosis are not completely understood yet, especially in a Chinese cohort.AIMTo investigate the relationship between gut mucosal microbiota profiles and CRC recurrence and patient prognosis.METHODSWe obtained the composition and structure of gut microbiota collected from 75 patients diagnosed with CRC and 26 healthy controls. The patients were followed up by regular examination to determine whether tumors recurred. Triplet-paired samples from on-tumor, adjacent-tumor and off-tumor sites of patients diagnosed with/without CRC recurrence were analyzed to assess spatial-specific patterns of gut mucosal microbiota by 16S ribosomal RNA sequencing. Next, we carried out bioinformatic analyses, Kaplan-Meier survival analyses and Cox regression analyses to determine the relationship between gut mucosal microbiota profiles and CRC recurrence and patient prognosis.RESULTSWe observed spatial-specific patterns of gut mucosal microbiota profiles linked to CRC recurrence and patient prognosis. A total of 17 bacterial genera/families were identified as potential biomarkers for CRC recurrence and patient prognosis, including Anaerotruncus, Bacteroidales, Coriobacteriaceae, Dialister, Eubacterium, Fusobacterium, Filifactor, Gemella, Haemophilus, Mogibacteriazeae, Pyramidobacter, Parvimonas, Porphyromonadaceae, Slackia, Schwartzia, TG5 and Treponema.CONCLUSIONOur work suggests that intestinal microbiota can serve as biomarkers to predict the risk of CRC recurrence and patient death.

Microcystin-leucine arginine induces skin barrier damage and reduces resistance to pathogenic bacteria in Lithobates catesbeianus tadpoles

Despite the importance of the skin mucosal barrier and commensal microbiota for the health of amphibians, the potential of environmental contaminants to disrupt the skin mucosal barrier and microbiota have rarely been studied in toxicology. In this study, tadpoles (Lithobates catesbeianus) were exposed to 0, 0.5, and 2 μg/L of microcystin-leucine arginine (MC-LR) for 30 days to explore the impacts of environmentally realistic MC-LR concentrations on the physical skin barrier, immune barrier, commensal microbiota, and skin resistance to pathogenic bacterial invasion. MC-LR exposure significantly reduced the collagen fibrils in the dermis of skin tissues and down-regulated tight junction and stratum corneum-related gene transcriptions, suggesting the damage caused by MC-LR to the physical barrier of the skin. Increased skin eosinophils and upregulated transcriptions of inflammation-related genes in the exposed tadpoles underline the development of skin inflammation resulting from MC-LR exposure even at environmentally realistic concentrations. Comparative transcriptome and immunobiochemical analyses found that antimicrobial peptides (Brevinin-1PLc, Brevinin-2GHc, and Ranatuerin-2PLa) and lysozyme were down-regulated in the exposed groups, while complement, pattern recognition receptor, and specific immune processes were up-regulated. However, the content of endotoxin lipopolysaccharide produced by bacteria increased in a dose-dependent pattern. The disc diffusion test showed a reduced ability of skin supernatant to inhibit pathogenic bacteria in the exposed groups. Analysis of microbial 16 S rRNA gene by high-throughput sequencing revealed that MC-LR interfered with the abundance, composition, and diversity of the skin commensal microbiota, which favored the growth of pathogen-containing genera Rhodococcus, Acinetobacter, and Gordonibacter. In summary, the current study provides the first clues about the impact of MC-LR on the integrity and function of skin barrier of amphibians. These new toxicological evidences can facilitate a more comprehensive evaluation of the ecological risk of MC-LR to amphibians.

Probiotic treatment vs empiric oral antibiotics for managing dysbiosis in short bowel syndrome: Impact on the mucosal and stool microbiota, short-chain fatty acids, and adaptation.

Infants and children with short bowel syndrome (SBS) are presumed to be at risk of gut microbial dysbiosis with potential sequelae of bacterial overgrowth that include sepsis, d-lactic acidosis, mucosal inflammation, and malabsorption. In neonatal piglets with SBS, we compared intestinal microbial composition, short-chain fatty acids (SCFAs), and adaptation given probiotic (PRO) treatment (Lactobacillus and Bifidobacterium spp) vs oral metronidazole (MET). Following 75% distal small intestinal resection, piglets were allocated to PRO (500 mg twice a day, n = 7), MET (15 mg/kg twice a day, n = 8), and placebo (PLA) (500 mg twice a day, n = 8). After 10 days of parenteral and enteral nutrition, 16S ribosomal RNA gene amplicon sequencing (colon tissue and stool) was undertaken and SCFA analysis (stool and colon effluent) was performed using gas chromatography. In colon, Shannon diversity was higher for PRO compared with MET and PLA (P = 0.002). PRO and PLA increased abundance of Bacteroidetes species (eg, Bacteroides fragilis) compared with MET (P < 0.001). PRO, compared with PLA, increased abundance of Firmicutes species (eg, Lactobacillus fermentum) (P < 0.001). MET increased abundance of Proteobacteria members, predominately Enterobacteriaceae, compared with PRO (P = 0.004). In stool, microbial findings were similar and SCFA (butyrate) concentrations were highest for PRO (P = 0.003) compared with MET. In pediatric SBS, the empiric use of oral antibiotics, such as MET, is common for presumed clinical consequences of microbial dysbiosis. In this study of SBS piglets, that approach was associated with decreased microbial diversity and increased abundance of potentially inflammatory Proteobacteria. In contrast, a PRO treatment using Lactobacillus and Bifidobacterium spp increased both diversity and SCFAs.

Three-dimensional imaging for the quantification of spatial patterns in microbiota of the intestinal mucosa

Improving our understanding of host–microbe relationships in the gut requires the ability to both visualize and quantify the spatial organization of microbial communities in their native orientation with the host tissue. We developed a systematic procedure to quantify the three-dimensional (3D) spatial structure of the native mucosal microbiota in any part of the intestines with taxonomic and high spatial resolution. We performed a 3D biogeographical analysis of the microbiota of mouse cecal crypts at different stages of antibiotic exposure. By tracking eubacteria and four dominant bacterial taxa, we found that the colonization of crypts by native bacteria is a dynamic and spatially organized process. Ciprofloxacin treatment drastically reduced bacterial loads and eliminated Muribaculaceae (or all Bacteroidetes entirely) even 10 d after recovery when overall bacterial loads returned to preantibiotic levels. Our 3D quantitative imaging approach revealed that the bacterial colonization of crypts is organized in a spatial pattern that consists of clusters of adjacent colonized crypts that are surrounded by unoccupied crypts, and that this spatial pattern is resistant to the elimination of Muribaculaceae or of all Bacteroidetes by ciprofloxacin. Our approach also revealed that the composition of cecal crypt communities is diverse and that Lactobacilli were found closer to the lumen than Bacteroidetes, Ruminococcaceae, and Lachnospiraceae, regardless of antibiotic exposure. Finally, we found that crypts communities with similar taxonomic composition were physically closer to each other than communities that were taxonomically different.

Heat Stress Weakens the Skin Barrier Function in Sturgeon by Decreasing Mucus Secretion and Disrupting the Mucosal Microbiota.

Heat stress induced by global warming has damaged the well-being of aquatic animals. The skin tissue plays a crucial role as a defense barrier to protect organism, however, little is known about the effect of heat stress on fish skin, particularly in cold-water fish species. Here, we investigated the effects of mild heat stress (24°C, MS) and high heat stress (28°C, HS) on Siberian sturgeon skin using RNA-seq, histological observation, and microbial diversity analysis. In RNA-seq, 8,819 differentially expressed genes (DEGs) in MS vs. C group and 12,814 DEGs in HS vs. C group were acquired, of which the MS vs. C and HS vs. C groups shared 3,903 DEGs, but only 1,652 DEGs were successfully annotated. The shared DEGs were significantly enriched in pathways associating with mucins synthesis. Histological observation showed that the heat stresses significantly reduced the number of skin mucous cells and induced the damages of epidermis. The microbial diversity analysis elicited that heat stress markedly disrupted the diversity and abundance of skin microbiota by increasing of potential pathogens (Vibrionimonas, Mesorhizobium, and Phyllobacterium) and decreasing of probiotics (Bradyrhizobium and Methylovirgula). In conclusion, this study reveals that heat stress causes adverse effects on sturgeon skin, reflecting in decreasing the mucus secretion and disordering the mucosal microbiota, which may contribute to develop the preventive strategy for heat stress caused by global warming.

Metagenomics analysis of cultured mucosal bacteria from colorectal cancer and adjacent normal mucosal tissues.

Introduction. Colorectal cancer (CRC) is one of the most common cancers worldwide. Multiple risk factors are involved in CRC development, including age, genetics, lifestyle, diet and environment. Of these, the role of the gut microbiota in cancer biology is increasingly recognized.Hypothesis/Gap Statement. Micro-organisms have been widely detected in stool samples, but few mucosal samples have been detected and sequenced in depth.Aim. Analysis of cultured mucosal bacteria from colorectal cancer and adjacent normal mucosal tissues with metagenomics sequencing.Methodology. Twenty-eight paired tumour and non-tumour tissues from 14 patients undergoing surgery for CRC were analysed. We removed the influence of eukaryotic cells via culture. The composition of mucosal microbiota in intestinal mucosa were detected and analysed with metagenomic sequencing.Results. Compared with non-cultured mucosal sample, 80 % bacteria species could be detected after culture. Moreover, after culture, additional 30 % bacteria could be detected, compared with non-cultured samples. Since after culture it was difficult to estimate the original abundance of microbiome, we focused on the identification of the CRC tissue-specific species. There were 298 bacterial species, which could only be cultured and detected in CRC tissues. Myroides odoratimimus and Cellulophaga baltica could be isolated from all the tumour samples of 14 CRC patients, suggesting that these species may be related to tumour occurrence and development. Further functional analysis indicated that bacteria from CRC tissues showed more active functions, including basic metabolism, signal transduction and survival activities.Conclusion. We used a new method based on culture to implement information on prokaryotic taxa, and related functions, which samples were from colorectal tissues. This method is suitable for removing eukaryotic contamination and detecting micro-organisms from other tissues.

ACTH(6-9)-Pro-Gly-Pro ameliorates anxiety-like and depressive-like behaviour and gut mucosal microbiota composition in rats under conditions of chronic restraint stress

The effects of the peptide ACTH(6–9)-Pro-Gly-Pro at doses of 5; 50; 500 μg/kg on the Wistar rats' behaviour and gut mucosal microbiota composition under conditions of chronic immobilization stress (CRS) were studied. CRS increased anxiety-like and depressive-like behaviour, disturbances in locomotor activity and gut dysbiosis. Administration of ACTH(6–9)-Pro-Gly-Pro showed many phenotypic results. Peptide demonstrated anti-depressant activity at doses of 5 and 500 μg/kg by a decrease in the total immobile time in the FST. ACTH(6–9)-Pro-Gly-Pro administered at a dose of 50 μg/kg resulted in an anxiolytic effect which is shown by an increase in the time in the open arms of EPM (p < 0.05) and a decrease in the time in the closed arms (p < 0.05). Moreover, the peptide led to a decrease in alpha- and beta-diversity of the gut microbiota (p < 0.01). Correlation and linear regression analysis demonstrated central mechanisms of ACTH(6–9)-Pro-Gly-Pro anxiolytic activity and both central and peripheral ones in an anti-depressant effect. In this way, peptide ACTH(6–9)-Pro-Gly-Pro could prevent the development of behavioural disturbances and gut dysbiosis caused by chronic restraint stress.

ORAL MICROBIOME INFLUENCES THE CLINICAL COURSE OF ORAL MUCOSITIS IN ALLOGENEIC HSCT PATIENTS

<h3>Objectives</h3> Oral mucositis (OM) is a complex acute cytotoxicity of antineoplastic treatment that affects 40% to 85% of patients undergoing hematopoietic stem cell transplantation. Clinically, OM is characterized by redness or ulceration covered by a pseudomembrane of cellular debris and bacterial colonies that usually develops within 5 to 7 days after the conditioning drug's administration. Incidence of OM is associated with prolonged hospitalization, extensive analgesic pharmacotherapy, parenteral nutrition, and elevated treatment costs. In this context, the identification of patient risks for OM is fundamental to enhance supportive care in oncology. OM onset relies on mucosal microenvironment status, with a possible role of microbiota-driven inflammation. We aimed to investigate whether the oral mucosa microbiota was associated with the clinical course of OM. <h3>Study Design</h3> We collected oral mucosa samples from 30 patients undergoing allogeneic hematopoietic stem cell transplantation at preconditioning. During the period of the study, 13 of 30 patients developed OM. For those patients, additional oral mucosa samples were collected at OM ulceration onset and ulcerated OM healing. All samples were characterized by 16S rRNA sequencing. <h3>Results</h3> We observed that specific taxa were associated with OM risk, severity, and time to resolution. In particular, at preconditioning, higher relative abundance of <i>Lactococcus</i> was associated with an increased ulcerated OM risk (75% vs 33%; <i>P</i> = .034), and the relative abundance of <i>Porphyromonas</i> was positively correlated with ulcerated OM grade (rho = 0.605, <i>P</i> = .028). Additionally, we observed that higher relative abundance of <i>Solobacterium</i> at OM onset was associated with prolonged OM ulcerated duration (<i>P</i> = .0005), whereas higher relative abundance of <i>Lactobacillus</i> was associated with shortened ulcerated OM duration (<i>P</i> = .032). <h3>Conclusions</h3> This was the first study to investigate oral mucosa taxa as biomarkers for OM clinical course in patients undergoing allogeneic hematopoietic stem cell transplantation. Our findings suggest that further research should focus on evaluating the influence of host-microbiome interactions on OM pathophysiology.

The Compositional Structure of the Small Intestinal Microbial Community via Balloon-Assisted Enteroscopy

Introduction: An association has been found between human-gut microbiota and various diseases (e.g., metabolic disease) by analyzing fecal or colonic microbiota. Despite the importance of the small intestinal microbiota, sampling difficulties prevent its full analysis. We investigated the composition and metagenomic functions of microbiota along the small intestine and compared them with the microbiota from feces and from other gastrointestinal (GI) sites. Methods: Mucosal samples from the six GI sites (stomach, duodenum, distal jejunum, proximal ileum, terminal ileum, and rectum) were collected under balloon-assisted enteroscopy. Fecal samples were collected from all participants. The microbial structures and metagenomic functions of the small intestinal mucosal microbiota were compared with those from feces and other GI sites using 16S ribosomal RNA gene sequencing. Results: We analyzed 133 samples from 29 participants. Microbial beta diversity analysis showed that the jejunum and ileum differed significantly from the lower GI tract and the feces (p < 0.001). Jejunal and duodenal microbiotas formed similar clusters. Wide clusters spanning the upper and lower GI tracts were observed with the ileal microbiota, which differed significantly from the jejunal microbiota (p < 0.001). Veillonella and Streptococcus were abundant in the jejunum but less so in the lower GI tract and feces. The metagenomic functions associated with nutrient metabolism differed significantly between the small intestine and the feces. Conclusions: The fact that the compositional structures of small intestinal microbiota differed from those of fecal and other GI microbiotas reveals that analyzing the small intestinal microbiota is necessary for association studies on metabolic diseases and gut microbiota.

Dietary Inclusion of Seabuckthorn (Hippophae rhamnoides) Mitigates Foodborne Enteritis in Zebrafish Through the Gut-Liver Immune Axis.

To help prevent foodborne enteritis in aquaculture, several feed additives, such as herbal medicine, have been added to fish diets. Predictions of effective herb medicines for treating fish foodborne enteritis from key regulated DEGs (differentially expressed genes) in transcriptomic data can aid in the development of feed additives using the Traditional Chinese Medicine Integrated Database. Seabuckthorn has been assessed as a promising candidate for treating grass carp soybean-induced enteritis (SBMIE). In the present study, the SBMIE zebrafish model was used to assess seabuckthorn’s therapeutic or preventative effects. The results showed that intestinal and hepatic inflammation was reduced when seabuckthorn was added, either pathologically (improved intestinal villi morphology, less oil-drops) or growth-related (body fat deposition). Moreover, seabuckthorn may block the intestinal p53 signaling pathway, while activating the PPAR signaling pathway and fatty acid metabolism in the liver. 16S rRNA gene sequencing results also indicated a significant increase in OTU numbers and skewed overlapping with the fish meal group following the addition of seabuckthorn. Additionally, there were signs of altered gut microbiota taxa composition, particularly for reduced TM7, Sphingomonas, and Shigella, following the addition of seabuckthorn. Hindgut imaging of fluorescent immune cells in SBMIE larvae revealed the immune regulatory mechanisms at the cellular level. Seabuckthorn may significantly inhibit the inflammatory gathering of neutrophils, macrophages, and mature T cells, as well as cellular protrusions’ formation. On the other hand, in larvae, seabuckthorn inhibited the inflammatory aggregation of lck+ T cells but not immature lymphocytes, indicating that it affected intestinal adaptive immunity. Although seabuckthorn did not affect the distribution of intestinal CD4+ cells, the number of hepatic CD4+ cells were reduced in fish from the seabuckthorn supplementation group. Thus, the current data indicate that seabuckthorn may alleviate foodborne gut-liver symptoms by enhancing intestinal mucosal immunity and microbiota while simultaneously inhibiting hepatic adipose disposition, making it a potential additive for preventing fish foodborne gut-liver symptoms.

Impact of Feeding Postbiotics and Paraprobiotics Produced From Lactiplantibacillus plantarum on Colon Mucosa Microbiota in Broiler Chickens.

This study was conducted to evaluate the impact of feeding postbiotics and paraprobiotics produced from Lactiplantibacillus plantarum on colon mucosa microbiota in broiler chickens. In this study, 336 one-day-old COBB 500 chicks were randomly allotted to eight treatment groups and replicated six times with seven birds per replicate. The treatment included T1 (Negative control) = Basal diet, T2 (Positive control) = Basal diet + 0.01% oxytetracycline, T3 = Basal diet + 0.2% postbiotic TL1, T4 = Basal diet + 0.2% postbiotic RS5, T5 = Basal diet + 0.2% paraprobiotic RG11, T6 = Basal diet + 0.2% postbiotic RI11, T7 = Basal diet + 0.2% paraprobiotic RG14, and T8 = Basal diet + 0.2% paraprobiotic RI11. There were reported changes in the bacterial community using 16S rRNA sequencing of the colon mucosa. The results of the sequencing of 16S rRNA genes in the colon mucosa samples indicated that compared to birds fed the negative control diet, birds fed paraprobiotic RI11 diets were recorded to have a lower relative abundance of Proteobacteria, while those fed the positive control were recorded to have a higher proportion of Firmicutes. Also, lower Enterococcus was reported in paraprobiotic RI11, while the most abundant genus was Bacteroides in postbiotic TL1. This study revealed that supplementation of postbiotics and paraprobiotics in the diets of broilers demonstrated positive effects on the microbiota by supporting the increase of beneficial microbes like the Firmicutes while decreasing harmful microbes like the Proteobacteria. Therefore, this study has provided knowledge on the modification of chicken mucosa microbiota through the feeding of postbiotics and paraprobiotics.

Comparative Evaluation of the Salivary and Buccal Mucosal Microbiota by 16S rRNA Sequencing for Forensic Investigations.

The human microbiome has emerged as a new potential biomarker for forensic investigations with the development of high-throughput sequencing and bioinformatic analysis during the last decade. The oral cavity has many different microbial habitats, with each habit colonized by specific and individualized microbiota. As saliva and buccal mucosa are common biological evidence in forensic science, understanding the differences of microbial communities between the two is important for forensic original identification. Moreover, the oral microbiota is individualized, whereas there are few studies on the application of forensic personal identification that need to be supplemented. In this study, Streptococcus was the most abundant genus, with an average relative abundance of 49.61% in the buccal mucosa, while in the saliva, Streptococcus, Veillonella, and Neisseria had similar proportions (20%, 15%, 16%) and were the dominant genera. The α and β diversity displayed a significant distinctness between the saliva and buccal mucosal groups. The community assembly mechanism stated that the deterministic process played a more significant effect in shaping the salivary bacterial community assembly than buccal mucosa, which explained the microbial differences. Of the test samples, 93.3% can be correctly classified with the random forest model based on the microbial differences. Targeting the low-abundance bacteria at the species level, 52% of experimental participants could be discriminated by using the observed unique bacterial species. In conclusion, the salivary bacterial community composition differed from that of the buccal mucosa and showed high richness and diversity. With the random forest model, the microbiota of saliva and buccal mucosa can be classified, which can be used in identifying the source of oral biological trace. Furthermore, each individual has a unique bacterial community pattern, and the presence or absence of unique bacteria and differences in the composition of the core oral microbiota are the key points for forensic personal discrimination that supplement the study of oral microbial application to forensic personal discrimination. Whether for original identification or personal discrimination, the oral microbiome has great potential for application.

Dysbiosis of Gastric Mucosal Fungal Microbiota in the Gastric Cancer Microenvironment.

Background Microbes have been shown to contribute to gastric cancer (GC), gastric bacteria and viruses are associated with gastric carcinogenesis. However, the relationship between gastric fungi and GC is still unclear. Our aim was to evaluate the gastric fungal microbiota in the GC microenvironment. Methods Gastric fungal microbiome profiling was performed with internal transcribed spacer (ITS) rDNA sequencing in primary tumor and corresponding paired normal mucosal tissues from 61 GC patients. Differences in microbial composition, taxa diversity, and predicted function were further analyzed. Results Dysbiosis of gastric mucosal fungal microbiome was observed between the tumor and normal groups in GC. The tumor group had a higher abundance of certain taxa than the normal group. In the taxa classification, the abundances of Pezizomycetes, Sordariales, Chaetomiaceae, and Rozellomycota were lower in the tumor group than in the normal group. At the genus level, Solicoccozyma (P = 0.033) was found in higher abundance and was differentially enriched in the tumor group with Lefse analysis. Additionally, Solicoccozyma accounted for 0.3% of gastric fungi in the GC microenvironment. Twenty-seven of the 61 GC patients showed positive Solicoccozyma expression in tumors. Solicoccozyma-positive expression in tumors was associated with the Bormann classification and nerve invasion. Solicoccozyma was considered a gastric fungal marker to classify stage I and stage II-IV GC patients with an area under the receiver-operating curve (AUC) of 0.7061, as well as to classify the nerve invasive and nonnerve invasive tumors from GC patients with an AUC of 0.6978. Functional prediction indicated that the positive expression of Solicoccozyma in tumors was associated with the amino acid- and carbohydrate-related metabolic pathways in GC. Conclusions This study revealed a novel perspective on the role of Solicoccozyma in tumors and a theoretical basis for therapeutic targets against GC.

Functional feeds marginally alter immune expression and microbiota of Atlantic salmon (Salmo salar) gut, gill, and skin mucosa though evidence of tissue-specific signatures and host\u2013microbe coadaptation remain

BackgroundMucosal surfaces of fish provide cardinal defense against environmental pathogens and toxins, yet these external mucosae are also responsible for maintaining and regulating beneficial microbiota. To better our understanding of interactions between host, diet, and microbiota in finfish and how those interactions may vary across mucosal tissue, we used an integrative approach to characterize and compare immune biomarkers and microbiota across three mucosal tissues (skin, gill, and gut) in Atlantic salmon receiving a control diet or diets supplemented with mannan-oligosaccharides, coconut oil, or both. Dietary impacts on mucosal immunity were further evaluated by experimental ectoparasitic sea lice (Lepeophtheirus salmonis) challenge.ResultsFish grew to a final size of 646.5 g ± 35.8 during the 12-week trial, with no dietary effects on growth or sea lice resistance. Bacterial richness differed among the three tissues with the highest richness detected in the gill, followed by skin, then gut, although dietary effects on richness were only detected within skin and gill. Shannon diversity was reduced in the gut compared to skin and gill but was not influenced by diet. Microbiota communities clustered separately by tissue, with dietary impacts on phylogenetic composition only detected in the skin, although skin and gill communities showed greater overlap compared to the gut according to overall composition, differential abundance, and covariance networks. Inferred metagenomic functions revealed preliminary evidence for tissue-specific host–microbiota coadaptation, as putative microbiota functions showed ties to the physiology of each tissue. Immune gene expression profiles displayed tissue-specific signatures, yet dietary effects were also detected within each tissue and peripheral blood leukocytes. Procrustes analysis comparing sample-matched multivariate variation in microbiota composition to that of immune expression profiles indicated a highly significant correlation between datasets.ConclusionsDiets supplemented with functional ingredients, namely mannan-oligosaccharide, coconut oil, or a both, resulted in no difference in Atlantic salmon growth or resistance to sea lice infection. However, at the molecular level, functional ingredients caused physiologically relevant changes to mucosal microbiota and host immune expression. Putative tissue-specific metagenomic functions and the high correlation between expression profiles and microbiota composition suggest host and microbiota are interdependent and coadapted in a tissue-specific manner.

The Spatial Landscape of the Bacterial Community and Bile Acids in the Digestive Tract of Patients With Bile Reflux.

BackgroundBile reflux can lead to inflammation and increased intestinal metaplasia. Since bile acids can influence the gastrointestinal environment, it is possible that bile reflux may alter the gastric microbiota and potentially the oral or gut microbiota. Bile acids have a very complex interrelationship with microbiota. We aimed to explore the characteristics of the digestive tract microbiota and bile acids profile in bile reflux patients.MethodsThis study included 20 chronic gastritis patients with bile reflux and 20 chronic gastritis patients without bile reflux. Saliva, gastric fluid, and fecal samples were collected for bile acid testing. Buccal mucosal swabs, gastric mucosal tissues, and feces were collected for bacteria detection. The UPLC-MS/MS examined bile acids profiles. 16S rRNA gene sequencing was used to analyze the bacterial profile.ResultsBilirubin in the blood increased in bile reflux patients. No other clinical factors were identified to be significantly associated with bile reflux. 12-DHCA, 6,7-diketo LCA, and βHDCA decreased while TUDCA increased in saliva of bile reflux patients. Streptococcus, Capnocytophaga, Neisseria, and Actinobacillus decreased in oral mucosa of bile reflux patients while Helicobacter, Prevotella, and Veillonella increased. Gastric bile acid levels were generally higher in bile reflux patients. Gastric mucosal microbiota was highly stable. The changes in fecal bile acids were insignificant. Bifidobacterium, Prevotella_2, Ruminococcus, Weissella, Neisseria, and Akkermansia decreased in fecal samples from bile reflux patients; while Alloprevotella, Prevotella_9, Parabacteroides, and Megamonas increased.ConclusionOur results demonstrate that bile reflux significantly alters the oral, gastric, and intestinal bile acids profiles but only influences the oral and gut microbiota composition. These findings indicate that bile reflux can modulate the gastrointestinal microbiota in a site-specific manner.