Colonization Of Gut Microbiota Research Articles

Gut microbiota is a hot and fast‐moving topic, and paediatricians need to monitor the latest developments

Gut microbiota is a hot and fast‐moving topic, and paediatricians need to monitor the latest developments

Early nutrition and gut microbiome: interrelationship between bacterial metabolism, immune system, brain structure, and neurodevelopment.

Disturbances of diet during pregnancy and early postnatal life may impact colonization of gut microbiota during early life, which could influence infant health, leading to potential long-lasting consequences later in life. This is a nonsystematic review that explores the recent scientific literature to provide a general perspective of this broad topic. Several studies have shown that gut microbiota composition is related to changes in metabolism, energy balance, and immune system disturbances through interaction between microbiota metabolites and host receptors by the gut-brain axis. Moreover, recent clinical studies suggest that an intestinal dysbiosis in gut microbiota may result in cognitive disorders and behavioral problems. Furthermore, recent research in the field of brain imaging focused on the study of the relationship between gut microbial ecology and large-scale brain networks, which will help to decipher the influence of the microbiome on brain function and potentially will serve to identify multiple mediators of the gut-brain axis. Thus, knowledge about optimal nutrition by modulating gut microbiota-brain axis activity will allow a better understanding of the molecular mechanisms involved in the crosstalk between gut microbiota and the developing brain during critical windows. In addition, this knowledge will open new avenues for developing novel microbiota-modulating based diet interventions during pregnancy and early life to prevent metabolic disorders, as well as neurodevelopmental deficits and brain functional disorders.

Early Intervention With Cecal Fermentation Broth Regulates the Colonization and Development of Gut Microbiota in Broiler Chickens.

The aim of this study was to investigate the effect of fermentation broth from broiler cecal content on the colonization and development of the gut microbiota in newly hatched broiler chicks. The fermentation broth was made by a chemostat system using the cecal content from a donor chicken as the source of inoculum. A total of 120 newly hatched broiler chicks were randomly divided into two groups. One group (F group) was orally inoculated with the fermentation broth, and the other (C group) was treated with an equal amount of sterile PBS solution. 16S rRNA gene sequencing was used to investigate the differences in the cecal microbiota of the broiler chickens between the two groups on days 1, 3, 7, 14, and 28. Moreover, the concentrations of short-chain fatty acids (SCFAs) in the cecal contents were analyzed by gas chromatography. The results showed that the abundances of genera Escherichia–Shigella and Enterococcus decreased sharply in the F group on days 1 and 3 by the early intervention with cecal fermentation broth. In contrast, the relative abundance of the genus Bacteroides on days 1, 3, and 7, and the family Ruminococcaceae on days 1, 3, and 28 increased in the F group, respectively. In terms of SCFAs, the concentrations of acetate on day 28, propionic acid on days 1, 3, 7, 14, and 28, butyrate on day 1, and isovalerate on day 14 were significantly higher in the F group compared with the C group. Overall, these results suggest that early intervention with cecal fermentation broth could have beneficial effects on broilers gut health, which might be attributed to the alterations in the gut microbial composition and the increased concentrations of SCFAs.

Characteristics of the gut microbiota colonization, inflammatory profile, and plasma metabolome in intrauterine growth restricted piglets during the first 12 hours after birth.

Intrauterine growth restriction (IUGR) predisposes newborns to inflammatory and metabolic disturbance. Disequilibrium of gut microbiota in early life has been implicated in the incidence of inflammation and metabolic diseases in adulthood. This study aimed to investigate the difference in gut microbiota colonization, cytokines and plasma metabolome between IUGR and normal birth weight (NBW) piglets in early life. At birth, reduced (P < 0.05) body, jejunum, and ileum weights, as well as decreased (P < 0.05) small intestinal villi and increased (P < 0.05) ileal crypt depth were observed in IUGR piglets compared with their NBW counterparts. Imbalanced inflammatory and plasma metabolome profile was observed in IUGR piglets. Furthermore, altered metabolites were mainly involved in fatty acid metabolism and inflammatory response. At 12 h after birth and after suckling colostrum, reduced (P < 0.05) postnatal growth and the small intestinal maturation retardation (P < 0.05) continued in IUGR piglets in comparison with those in NBW littermates. Besides, the gut microbiota structure was significantly altered by IUGR. Importantly, the disruption of the inflammatory profile and metabolic status mainly involved the pro-inflammatory cytokines (IL-1β and IFN-γ) and amino acid metabolism. Moreover, spearman correlation analysis showed that the increased abundance of Escherichia-Shigella and decreased abundance of Clostridium_sensu_stricto_1 in IUGR piglets was closely associated with the alterations of slaughter weight, intestinal morphology, inflammatory cytokines, and plasma metabolites. Collectively, IUGR significantly impairs small intestine structure, modifies gut microbiota colonization, and disturbs inflammatory and metabolic profiles during the first 12 h after birth. The unbalanced gut microbiota mediated by IUGR contributes to the development of inflammation and metabolic diseases.

Preterm Birth Has Effects on Gut Colonization in Piglets Within the First 4 Weeks of Life.

Preterm neonates have an immature gastrointestinal tract and show an altered bacterial colonization of the gut. However, it is not clear if such immature gut microbiota (GM) colonization is induced by specific delivery, diet, environment, and/or host factors related to preterm birth. Using piglets as models for infants, we hypothesized that both shortened gestational age (GA) and start of enteral feeding affect GM composition after caesarean delivery and rearing in identical environments. Caesarean-delivered preterm and term pigs were reared in incubators and fed total parenteral nutrition (TPN) or gradually increasing early enteral feeding (EEF) for 5 days, followed by full enteral feeding with bovine milk until day 26. GM composition was determined by 16S rRNA gene-amplicon sequencing and luminal short-chain fatty acids (SCFAs) by GC-MS. Both GA and EEF feeding affected GM composition on day 5, but only the GA effect persisted until day 26. On day 5, Enterobacteriaceae were dominant, with Lachnospiraceae members also being abundant. Enterobacteriaceae still dominated the GM at day 26 but with higher Akkermansia relative abundance in term pigs. Colonic concentrations of acetate and propionate were higher, and formate lower in term pigs, relative to preterm pigs on day 26. Preterm and term piglets, born and reared in similar ways, show differences in GM colonization during the first 4 weeks of life, which may play a role for early and later gut dysfunction resulting from preterm birth.

Impact of Early Exposure to Cefuroxime on the Composition of the Gut Microbiota in Infants Following Cesarean Delivery

To assess in mothers giving birth by cesarean delivery if prophylactic antibiotics administered either before skin incision or immediately after cutting the umbilical cord influences gut microbiota colonization and antibiotic susceptibility of the gut bacteria in the newborn. Forty-two pregnant women scheduled for elective cesarean delivery were recruited at Odense University Hospital, Denmark, and randomly assigned to receive cefuroxime either before skin incision or immediately after the umbilical cord was cut. Fecal samples were collected from all infants at age 10days and 9months. Composition of the gut microbiota was determined by 16S ribosomal RNA gene amplicon high-throughput sequencing. Gram-positive cocci and Enterobacteriaceae were isolated and identified before antimicrobial susceptibility tests were performed by disk diffusion. No clear difference in the composition of the gut microbiota was observed between infants whose mothers received cefuroxime before or after cesarean delivery at neither time point, though surprisingly at 9months of age, but not at 10days of age, the number of observed species was higher in infants where mothers received cefuroxime after cord clamping. No differences in antimicrobial susceptibility of Enterobacteriaceae, Enterococcus spp, and Staphylococcus spp were seen at 10days. Timing of cefuroxime administration to mothers undergoing cesarean delivery does not have a major effect on the gut microbiota and bacterial antibiotic resistance traits in infants. Clinicaltrials.gov: NCT02072798.

Gut Microbiota Shifts in Pup Athymic BALB/c Mice: An Updated Identification in Nude Mice.

Simple SummaryMammal gut microbiota has been gradually considered to be related to innate and adaptive immunity. Incredibly, although athymic nude mouse is one of the most popular animals for modeling immunodeficiency and tumors, a basic understanding of its gut microbiota has still not been attained, and current relevant conclusions are controversial. In this 30-day study, based on high-throughput sequencing technology, we compared the differences in gut microbial community structures and functions between normal and nude pup mice, and concluded that gut microbiota shifts did occur in nude mice. These findings provide updated insight for the nude mouse tumor model.It is commonly recognized that immunodeficiency modifies the gut microbiota in mammals. However, little information on the gut microbiota is available for athymic nude mice; one of the most popular animals for modeling immunodeficiency and tumors. In this study, 16S rDNA amplicon sequencing was performed to investigate the gut microbial composition of pup nude BALB/c mice during a 30-day experimental period. In contrast to pup normal mice, pup nude mice showed a significant variation in gut microbiota. Continuously decreased dynamics of the gut bacterial Shannon index, abnormal Firmicutes/Bacteroidetes ratio, the rarity of Bifidobacterium and Lactobacillus species, and a developmental lag of gut bacterial functions were observed in nude mice. The shift in gut microbiota and abnormal colonization of beneficial bacterial species in nude mice provide an updated insight into the nude mouse tumor model and a new perspective for establishing an animal model for study on dysbacteriosis.

Probiotics and Prebiotics for the Amelioration of Type 1 Diabetes: Present and Future Perspectives.

Type 1-diabetes (T1D) is an autoimmune disease characterized by immune-mediated destruction of pancreatic beta (β)-cells. Genetic and environmental interactions play an important role in immune system malfunction by priming an aggressive adaptive immune response against β-cells. The microbes inhabiting the human intestine closely interact with the enteric mucosal immune system. Gut microbiota colonization and immune system maturation occur in parallel during early years of life; hence, perturbations in the gut microbiota can impair the functions of immune cells and vice-versa. Abnormal gut microbiota perturbations (dysbiosis) are often detected in T1D subjects, particularly those diagnosed as multiple-autoantibody-positive as a result of an aggressive and adverse immunoresponse. The pathogenesis of T1D involves activation of self-reactive T-cells, resulting in the destruction of β-cells by CD8+ T-lymphocytes. It is also becoming clear that gut microbes interact closely with T-cells. The amelioration of gut dysbiosis using specific probiotics and prebiotics has been found to be associated with decline in the autoimmune response (with diminished inflammation) and gut integrity (through increased expression of tight-junction proteins in the intestinal epithelium). This review discusses the potential interactions between gut microbiota and immune mechanisms that are involved in the progression of T1D and contemplates the potential effects and prospects of gut microbiota modulators, including probiotic and prebiotic interventions, in the amelioration of T1D pathology, in both human and animal models.

Effects of Antibiotics on the Development and Colonization of Preterm Gut Microbiota: A Short Review

The gut microbiota plays a vital role in the development of the immune system, nutrient absorption, and resistance to pathogen colonization. Antibiotics are among the many factors that affect and influence the establishment of the microbiota., Neonates, particularly those born prematurely, represent an interesting population because they receive early and often extensive antibiotic therapy in the first year of life. It is important to understand the effects of these antibiotics in reshaping and colonization of intestinal microbiome. Antibiotic therapy in preterm infants can dramatically affect the gut microbiome. Early establishment of the gut microbiome is suspected to have a particularly profound impact in protecting the gut from infectious disease and on long-term subsequent health by predisposing individuals to atopic or autoimmune disease later in life. This review gathers relevant literatures on the effects of antibiotics on the preterm gut microbiota both on their composition and development. This review indicates that some antibiotic treatments are associated with decreased species richness and diversity. Treatment with antibiotic encouraged resistance genes and proliferation of multidrug resistant organisms. Antibiotics regimens bring about population shifts and reshape the abundant microbial colonization. We therefore, demonstrated the impact of antibiotics on the composition of microbial community and its establishment from the gut of preterm infants during their early days of life.

Human Breast-Milk Feeding Enhances the Humoral and Cell-Mediated Immune Response in Neonatal Piglets

BackgroundThe benefits of breastfeeding infants are well characterized, including those on the immune system. However, determining the mechanism by which human breast milk (HBM) elicits effects on immune response requires investigation in an appropriate animal model. ObjectiveThe primary aim of this study was to develop a novel porcine model and to determine the differential effects of feeding HBM and a commercial milk formula (MF) on immune response and gastrointestinal microbial colonization in a controlled environment. MethodsMale piglets were fed HBM (n = 26) or MF (n = 26) from day 2 through day 21. Piglets were vaccinated (n = 9/diet group) with cholera toxin and cholera toxin subunit B (CTB) and tetanus toxoid at 21 d or were fed placebo (n = 6/diet group) and then weaned to a standard solid diet at the age of 21 d. Humoral and cell-mediated immune responses were assessed from blood on days 35 and 48. Immune response was further examined from tissues, including mesenteric lymph nodes (MLNs), Peyer's patches (PPs), and spleen. The colonization of gut microbiota was characterized from feces on days 16 and 49. ResultsSerum antibody titers in piglets fed HBM were 4-fold higher (P < 0.05) to CTB and 3-fold higher (P < 0.05) to tetanus toxoid compared with piglets fed MF on day 48. Compared with MF, the numbers of immunoglobulin A antibody–producing cells to CTB were 13-fold higher (P < 0.05) in MLNs and 11-fold higher (P < 0.05) in PPs in the HBM diet group on day 51. In addition, significantly increased T cell proliferation was observed in the HBM group relative to the MF group. Furthermore, microbial diversity in the HBM group was lower (P < 0.05) than in the MF group. ConclusionThis porcine model appears to be valid for studying the effects of early postnatal diet on immune responses and the gastrointestinal microbiome. Our results lay the groundwork for future studies defining the role of infant diet on microbiota and immune function.

Fetal cardiac growth is associated with in utero gut colonization

Background and aimsIntra-uterine metabolic environment predicts newborns’ cardiac morphology, metabolism and future health. In adults, gut microbiota composition relates to altered cardiac structure and metabolism. We investigated the relationship between gut microbiota colonization and fetal cardiac growth. Methods and resultsBacterial composition in meconium samples of 26 healthy, full-term newborns was assessed by 16S rDNA gene sequencing. Its relationship with birth echocardiographic parameters, and the interaction with cord blood levels of inflammatory markers were investigated. Correlative and cluster analysis, linear discriminant analysis effect size and predictive functional analysis based on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were applied. Fetal left ventricle growth was related to gut microbiota composition at birth. Specifically, left ventricle posterior wall thickness (LVPW) greater than 4 mm was associated with lower microbiota beta and alpha diversity, depletion (LDA score > 3) of several bacteria at each taxonomic level, including Lactobacillales, and enrichment (LDA score > 5) in Enterobacteriales and Enterobacteriaceae. The latter was significantly related to cord blood gamma-glutamyltransferase levels (r = 0.58, p = 0.0057). Functionally, a thicker LVPW was related to up-regulation of pathways involved in lipopolysaccharide biosynthesis (+50%, p = 0.045 in correlative analysis) and energy metabolism (+12%, p = 0.028), and down-regulation of pathways involved in xenobiotic biodegradation (−21 to −53%, p = 0.0063–0.039), PPAR signaling (−24%, p = 0.021) and cardiac muscle contraction (−100%, p = 0.049). ConclusionFetal cardiac growth and gut colonization are associated. Greater neonatal LVPW thickness is related to lower diversity of the gut microbiota community, depletion of bacteria having anti-remodeling effects, and enrichment in bacteria functionally linked to inflammation.

Microbiota and Derived Parameters in Fecal Samples of Infants with Non-IgE Cow's Milk Protein Allergy under a Restricted Diet.

Cow’s milk protein allergy (CMPA) is the most common food allergy in infancy. Non-IgE mediated (NIM) forms are little studied and the responsible mechanisms of tolerance acquisition remain obscure. Our aim was to study the intestinal microbiota and related parameters in the fecal samples of infants with NIM-CMPA, to establish potential links between type of formula substitutes, microbiota, and desensitization. Seventeen infants between one and two years old, diagnosed with NIM-CMPA, were recruited. They were all on an exclusion diet for six months, consuming different therapeutic protein hydrolysates. After this period, stool samples were obtained and tolerance development was evaluated by oral challenges. A control group of 10 age-matched healthy infants on an unrestricted diet were included in the study. Microbiota composition, short-chain fatty acids, calprotectin, and transforming growth factor (TGF)-β1 levels were determined in fecal samples from both groups. Infants with NIM-CMPA that consumed vegetable protein-based formulas presented microbiota colonization patterns different from those fed with an extensively hydrolyzed formula. Differences in microbiota composition and fecal parameters between NIM-CMPA and healthy infants were observed. Non-allergic infants showed a significantly higher proportion of Bacteroides compared to infants with NIM-CMPA. The type of protein hydrolysate was found to determine gut microbiota colonization and influence food allergy resolution in NIM-CMPA cases.

Resistant Starch Supplementation Improves Bifidobacteria Colonization and Lipid Profile in Adult Obese Subjects Residing in Urban Vadodara

Obesity continues to be a growing problem globally among all age groups, further associated with life threatening co-morbidities. Resistant Starch (RS) as a dietary component has been recently recognized as a prebiotic with potential role in improving the bacterial ecology of human gut. The present study was undertaken to evaluate the impact of resistant starch supplementation by the obese adults in urban Vadodara on microbial changes in gut flora with respect to Bifidobacteria and Enterobacteria. Using a non randomised control trial study design, 60 obese adults were enrolled from the free living population of urban Vadodara. Baseline information was collected and subjects were classified into control (n=30) and experimental group (n=30). Experimental group was supplemented with 10 g of RS daily for the period of two months (60 days). The control group were not given anything during this period. Blood and stool samples were analysed for lipid profile and the presence of Bifidobacteria and pathogenic Enterobacteria, respectively both at baseline and after the intervention period. Results revealed a significant increase in the mean log counts of Bifidobacteria by 11.7% with no significant reduction in the mean log counts of enteric pathogens and lipid profile of subjects. Hence study concludes that a daily supplementation of 10 grams of RS for 60 days to the obese subjects improved colonization of beneficial gut microbiota in terms of Bifidobacteria, but had little effect on obesity.

Gut Microbiota and Mucosal Immunity in the Neonate.

Gut microbiota colonization is a complex, dynamic, and step-wise process that is in constant development during the first years of life. This microbial settlement occurs in parallel with the maturation of the immune system, and alterations during this period, due to environmental and host factors, are considered to be potential determinants of health-outcomes later in life. Given that host–microbe interactions are mediated by the immune system response, it is important to understand the close relationship between immunity and the microbiota during birth, lactation, and early infancy. This work summarizes the evidence to date on early gut microbiota colonization, and how it influences the maturation of the infant immune system and health during the first 1000 days of life. This review will also address the influence of perinatal antibiotic intake and the importance of delivery mode and breastfeeding for an appropriate development of gut immunity.

Influences of different microbial environment on gut microbiota colonization in early life of mice

Objective To investigate the influences of exposure to different environmental microbes on early-life gut microbiota colonization in mice. Methods Male (n=8) and female (n=16) adult specific pathogen free (SPF) BALB/c mice were caged together at a ratio of 2∶1. After conception, the mice were divided into four groups according to the environments where the offsprings were reared at three different periods (fetal period, breastfeeding period and childhood). Group A: Offsprings were kept in a SPF environment throughout the study; group B: SPF environment during fetal and breastfeeding periods, and then ordinary environment during childhood; group C: SPF environment during fetal period, and then ordinary environment during breastfeeding period and childhood; group D: ordinary environment all the time. Fecal samples were collected at the end of week 3 and 5. Total bacterial DNA was extracted from each sample and analyzed by high throughput analysis. Kruskal-Wallis and Dunn-Bonferroni test were applied for statistical anaysis. Results 1. At the end of three weeks: (1) Diversity:① Phylum level: There were significant differences in the abundance of Firmicutes, Verrucomicrobia, Proteobacteria and Actinobacteria among the four group (all P 0.05). The OTUs of group A and B were significantly lower than that of group D [246(221-348), 257(209-280) vs 387(324-478), P=0.045 and 0.008, respectively]. 2. At the end of five weeks: (1) Diversity:① Phylum level: There were significant differences in the abundance of Firmicutes, Verrucomicrobia and Proteobacteria among the four groups (P<0.05 or 0.01). The abundance of Firmicutes in gut microbiota in group A was lower than that in group B, C and D [13.765(64.181-24.238)×10-2 vs 48.912(37.280-59.466)×10-2, 86.065(50.149-89.856)×10-2, 53.847(31.946-72.936)×10-2], while that of Verrucomicrobia was higher [58.089(22.459-61.285)×10-2 vs 0.001(0.000-0.005)×10-2, 0.000(0.000-0.001)×10-2, 0.003(0.000-0.006)×10-2], all P<0.05 or 0.01.② Genus level: There were significant differences in the abundance of Lactobacillus and Akkermansia among the four groups (P<0.01).The abundance of Lactobacillus in gut microbiota in group A was lower than that in group B, C and D[1.755(0.805-8.833)×10-2 vs 26.391(17.550-37.265)×10-2, 70.688(45.713-77.953)×10-2, 28.675(15.660-57.224)×10-2], while that of Akkermansia was higher [58.089(22.460-61.285)×10-2 vs 0.000(0.000-0.006)×10-2, 0.000(0.000-0.001)×10-2, 0.003(0.000-0.006)×10-2, all P<0.05 or 0.01]. (2) Alpha diversity: There were significant differences in OTU, Chao1 and Shannon index among the four groups (P<0.05 or 0.01). The OTU of group A was lower than that of group B, C and D [268(241-410) vs 438(380-516), 562(533-588), 546(473-599)], and the OTU, Chao1 and Shannon index of group B were all lower than those of group C and D [OTU: 438(380-516) vs 562(533-588), 546(473-599); Chao1 index: 1 033(883-1 181) vs 1 285(1 220-1 338), 1 328(1 155-1 516); Shannon index: 3.85(3.25-4.50) vs 4.28(3.30-5.11), 4.17(3.62-4.38), all P<0.05 or 0.01]. Conclusions Early-life exposure to different environments has an obvious impact on the diversity and composition of intestinal microbiota in mice. The less clean the living environment is, the more diverse the gut microflora will be. Furthermore, the window of opportunity for gut microbiota colonization seems to be related to breastfeeding period. Key words: Animals, suckling; Animals, newborn; Gastrointestinal microbiome; Environmental exposure; Biodiversity

Factors affecting colonization of maternal and fetal gut microbiota during perinatal period

Human gut microbiota contains around 1014 colonized intestinal microbes. Gut microbiome outnumbers the human gene pool by ten to one. Therefore, it's generally considered to be our second gene pool. Several research have clarified that the cycle of intestinal microbes-placental microbes-fetal intestinal microbes plays a critical role in the neurological and immune regulation and metabolism in infants, which may contribute to the furtherance of research on gut microbes. We summarized the factors affecting the colonization of maternal and fetal gut microorganisms during perinatal period from recent research. Key words: Perinatal period; Gastrointestinal microbiome

Drosophila melanogaster establishes a species-specific mutualistic interaction with stable gut-colonizing bacteria.

Animals live together with diverse bacteria that can impact their biology. In Drosophila melanogaster, gut-associated bacterial communities are relatively simple in composition but also have a strong impact on host development and physiology. It is generally assumed that gut bacteria in D. melanogaster are transient and their constant ingestion with food is required to maintain their presence in the gut. Here, we identify bacterial species from wild-caught D. melanogaster that stably associate with the host independently of continuous inoculation. Moreover, we show that specific Acetobacter wild isolates can proliferate in the gut. We further demonstrate that the interaction between D. melanogaster and the wild isolated Acetobacter thailandicus is mutually beneficial and that the stability of the gut association is key to this mutualism. The stable population in the gut of D. melanogaster allows continuous bacterial spreading into the environment, which is advantageous to the bacterium itself. The bacterial dissemination is in turn advantageous to the host because the next generation of flies develops in the presence of this particularly beneficial bacterium. A. thailandicus leads to a faster host development and higher fertility of emerging adults when compared to other bacteria isolated from wild-caught flies. Furthermore, A. thailandicus is sufficient and advantageous when D. melanogaster develops in axenic or freshly collected figs, respectively. This isolate of A. thailandicus colonizes several genotypes of D. melanogaster but not the closely related D. simulans, indicating that the stable association is host specific. This work establishes a new conceptual model to understand D. melanogaster–gut microbiota interactions in an ecological context; stable interactions can be mutualistic through microbial farming, a common strategy in insects. Moreover, these results develop the use of D. melanogaster as a model to study gut microbiota proliferation and colonization.

Gut bacterial assemblages of freshwater macroinvertebrate functional feeding groups

Little is known about the impacts of diet and environment on the composition and stability of gut microbial assemblages among freshwater macroinvertebrate functional feeding groups, compared to terrestrial counterparts. In this study, we compared gut microbial assemblages among functional feeding groups and environmental/dietary materials (biofilm and bacterioplankton) within and across two Northeastern Ohio streams differing in environmental conditions, following partial 16S rRNA sequence data analyses. Four functional feeding groups (filter feeders, grazers/collectors, omnivores, and predators) were uncovered in both streams, with significant differences in gut microbial community compositions among functional feeding groups within streams, and significant similarities in gut microbial community compositions between the same functional feeding groups across streams. Observed differences and similarities among functional feeding groups may be attributed to group-specific internal sorting processes due to physical and chemical properties (such as pH and oxygen levels) of the gut, which impact successful bacterial colonization. Results from this study provide insights into the impacts of diet and environment on the composition and stability of freshwater macroinvertebrate gut microbial assemblages. Results also provide a basis for further studies investigating initial establishment and colonization of gut microbiota across developmental stages, and potential gut microbial functions of importance to freshwater macroinvertebrate hosts.

Wisconsin microbiome study, a cross-sectional investigation of dietary fibre, microbiome composition and antibiotic-resistant organisms: rationale and methods

IntroductionPrevention of multidrug-resistant organism (MDRO) infections, such as those caused by methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci, fluoroquinolone-resistant Gram-negative bacteria and Clostridium difficile is crucial. Evidence suggests that dietary fibre increases...

Goblet cell associated antigen passages are inhibited during Salmonella typhimurium infection to prevent pathogen dissemination and limit responses to dietary antigens.

Dietary antigen acquisition by lamina propria (LP) dendritic cells (DCs) is crucial to induce oral tolerance and maintain homeostasis. However, encountering innocuous antigens during infection can lead to inflammatory responses, suggesting processes may limit steady-state luminal antigen capture during infection. We observed that goblet cell (GC) associated antigen passages (GAPs), a steady-state pathway delivering luminal antigens to LP-DCs, are inhibited during Salmonella infection. GAP inhibition was mediated by IL-1β. Infection abrogated luminal antigen delivery and antigen specific T cell proliferation in the mesenteric lymph node (MLN). Antigen specific T cell proliferation to dietary antigen was restored by overriding GAP suppression; however, this did not restore regulatory T cell induction but induced inflammatory T cell responses. Salmonella translocation to the MLN required GCs and correlated with GAPs. Genetic manipulations overriding GAP suppression, or antibiotics inducing colonic GAPs, but not antibiotics that don’t, increased dissemination and worsened outcomes independent of luminal pathogen burden. Thus, steady-state sampling pathways are suppressed during infection to prevent responses to dietary antigens, limit pathogen entry, and lessen disease. Moreover, antibiotics may worsen Salmonella infection by means beyond blunting gut microbiota colonization resistance, providing new insight into how precedent antibiotic use aggravates enteric infection.