Intestinal microbiome profiles in broiler chickens raised without antibiotics exhibit altered microbiome dynamics relative to conventionally raised chickens

The present study was undertaken to profile and compare the cecal microbial communities in conventionally (CONV) grown and raised without antibiotics (RWA) broiler chickens. Three hundred chickens were collected from five CONV and five RWA chicken farms on days 10, 24, and 35 of age. Microbial genomic DNA was extracted from cecal contents, and the V4-V5 hypervariable regions of the 16S rRNA gene were amplified and sequenced. Analysis of 16S rRNA sequence data indicated significant differences in the cecal microbial diversity and composition between CONV and RWA chickens on days 10, 24, and 35 days of age. On days 10 and 24, CONV chickens had higher richness and diversity of the cecal microbiome relative to RWA chickens. However, on day 35, this pattern reversed such that RWA chickens had higher richness and diversity of the cecal microbiome than the CONV groups. On days 10 and 24, the microbiomes of both CONV and RWA chickens were dominated by members of the phylum Firmicutes. On day 35, while Firmicutes remained dominant in the RWA chickens, the microbiome of CONV chickens exhibited am abundance of Bacteroidetes. The cecal microbiome of CONV chickens was enriched with the genus Faecalibacterium, Pseudoflavonifractor, unclassified Clostridium_IV, Bacteroides, Alistipes, and Butyricimonas, whereas the cecal microbiome of RWA chickens was enriched with genus Anaerofilum, Butyricicoccu, Clostridium_XlVb and unclassified Lachnospiraceae. Overall, the cecal microbiome richness, diversity, and composition were greatly influenced by the management program applied in these farms. These findings provide a foundation for further research on tailoring feed formulation or developing a consortium to modify the gut microbiome composition of RWA chickens.

A type 4 resistant potato starch alters the cecal microbiome and gene expression in mice fed a western diet based on NHANES data

Four major types of resistant starch (RS1-4) are present in foods, all of which can alter the microbiome and are fermented in the cecum and colon to produce short-chain fatty acids (SCFAs). Type 4 RSs are chemically modified starches, not normally found in foods, but have become a popular food additive as their addition increases fiber content. Multiple studies, in humans and rodents, have explored how different RS4 affect post-prandial glucose metabolism, but fewer studies have examined the effects of RS4 consumption on the microbiome. In addition, many RS studies conducted in rodents use high-fat diets that do not approximate what is typically consumed by humans. To address this, mice were fed a Total Western Diet (TWD), based on National Health and Nutrition Examination Survey (NHANES) data that mimics the macro and micronutrient composition of a typical American diet, for six weeks, and then supplemented with 0, 2, 5, or 10% of the RS4, Versafibe 1490™ (VF), a phosphorylated and cross-linked potato starch, for an additional three weeks. The cecal contents were analyzed for SCFA content and microbiota composition. Butyrate production was increased while branched chain SCFA production decreased. The alpha-diversity of the microbiome decreased in mice fed the TWD with 10% VF 1490 added while the beta-diversity plot showed that the 5% and 10% VF groups were distinct from mice fed the TWD. Similarly, the largest changes in relative abundance of various genera were greatest in mice fed the 10% VF diet. To examine the effect of VF consumption on tissue gene expression, cecal and distal colon tissue mRNA abundance were analyzed by RNASeq. Gene expression changes were more prevalent in the cecum than the colon and in mice fed the 10% VF diet, but the number of changes was substantially lower than we previously observed in mice fed the TWD supplemented with native potato starch (RPS). These results provide additional evidence that the structure of the RS is a major factor determining its effects on the microbiome and gene expression in the cecum and colon.

Impacts of willow (Salix babylonica L.) leaf extract on growth, cecal microbial population, and blood biochemical parameters of broilers

The investigation examined the use of willow leaf extract (WLE) on broiler chickens, examining carcass characteristics, cecal microbiota, antioxidants, and blood parameters. In 4 groups of 300 chicks, a basal diet was given for 5 wk, and the first treatment was basal diet (C). The diets for the remaining 3 treatments (WLE150, WLE300, and WLE450) contained 150, 300, and 450 mg of willow leaf extract /kg, respectively. The study found that birds fed willow leaf extract supplements had significantly greater body weight (BW), body weight gain (BWG), and enhanced feed conversion ratio (FCR) vs. the control group. Birds fed at 450 mg/kg food showed the greatest growth features, carcass weight, liver weight, lower abdominal fat, better low-density lipoprotein (LDL), and high-density lipoprotein (HDL) concentrations, and highest hematological characteristics. Chickens fed diets supplemented with varied doses of willow leaf extract showed significantly increased antioxidant enzyme activity, with higher amounts of glutathione peroxidase (GPx) activity, superoxide dismutase (SOD), total antioxidant capacity (TAC), and lower malondialdehyde (MDA). However, in the study, birds fed a diet supplemented with 450 mg of willow leaf extract per kg meal showed a significant drop of 13.02%, which found no significant variations in hazardous bacteria (Escherichia coli) across 2 treatments (WLE150 and WLE300). In addition, the study discovered that birds fed with varied doses of willow leaf extract had fewer cecum infections (Staphylococci aureus). We conclude that using willow at a level of 450 mg/kg diet can significantly enhance the BWG, FCR, antioxidant levels and beneficial bacteria activity besides the condition of broiler chicken's general health.

Effects of different supplemental levels of protease DE200 on the production performance, egg quality, and cecum microflora of laying hens

This study aimed to investigate the effects of different levels of the protease DE200 on the performance, egg quality, organ index, and cecum microflora of Hy-line W36 laying hens. In this experiment, a total of 180 laying hens aged 300 d were randomly divided into three treatment groups and fed diets containing 0, 100, or 200 g/t DE200. The experimental period was 8 wk, including 2 wk of prefeeding and 6 wk of the formal experiment. Regular feeding was performed thrice a day and eggs were collected twice daily, and the feed intake and the egg quality were recorded. The results showed that in terms of production performance, dietary supplementation with different levels of DE200 significantly increased egg production (EP; P < 0.05) and significantly decreased the feed conversion ratio (FCR; P < 0.05) and average daily feed intake (ADFI; P < 0.05) without affecting egg weight (EW). In addition, the addition of DE200 significantly reduced the egg breakage rate (P < 0.05) and tended to increase the Haugh unit and decrease the water content of the yolk (P > 0.05). In the cecal microflora, the addition of DE200 increased the proportions of Bacteroidetes and Firmicutes at the phylum level while reducing the proportion of Fusobacteria. Furthermore, at the genus level, the addition of DE200 increased the proportions of Bacteroides and Faecalibacterium and reduced the proportion of Megamonas. This study suggested that the protease DE200 can be used as a feed supplement to improve the production performance of laying hens.

Colonization of chickens with competitive exclusion products results in extensive differences in metabolite composition in cecal digesta

The concept of competitive exclusion is well established in poultry and different products are used to suppress the multiplication of enteric pathogens in the chicken intestinal tract. While the effect has been repeatedly confirmed, the specific principles of competitive exclusion are less clear. The aim of the study was to compare metabolites in the cecal digesta of differently colonized chickens. Metabolites in the cecal contents of chickens treated with a commercial competitive exclusion product or with an experimental product consisting of 23 gut anaerobes or in control untreated chickens were determined by mass spectrometry. Extensive differences in metabolite composition among the digesta of all 3 groups of chickens were recorded. Out of 1,706 detected compounds, 495 and 279 were differently abundant in the chicks treated with a commercial or experimental competitive exclusion product in comparison to the control group, respectively. Soyasaponins, betaine, carnitine, glutamate, tyramine, phenylacetaldehyde, or 3-methyladenine were more abundant in the digesta of control chicks while 4-oxododecanedioic acid, nucleotides, dipeptides, amino acids (except for glutamate), and vitamins were enriched in the digesta of chickens colonized by competitive exclusion products. Metabolites enriched in the digesta of control chicks can be classified as of plant feed origin released in the digesta by degradative activities of the chicken. Some of these molecules disappeared from the digesta of chicks colonized by complex microbiota due to them being metabolized. Instead, nucleotides, amino acids, and vitamins increased in the digesta of colonized chicks as a consequence of the additional digestive potential brought to the cecum by microbiota from competitive exclusion products. It is therefore possible to affect metabolite profiles in the chicken cecum by its colonization with selected bacterial species.

Research Note: Intestinal avian defensin 2 and robustness of chicks

Poultry production is an important agricultural sector for human food worldwide. Chicks after hatch often face health problems leading to economic losses that are deleterious for breeders. Avian defensin 2 (AvBD2) is a prominent host defense peptide of the intestinal mucosa of cecum and is involved in the resistance of poultry to bacterial pathogens. This peptide could thus represent an innate immunity marker of robustness of birds. To test this hypothesis by comparing fast-growing and slow-growing lines in different conditions of breeding, the chick's cecal AvBD2 content was analyzed according to animal quality and immunity indicators. Chick's cecal tissue sections labeled by immunohistochemistry with newly developed specific antibodies revealed the localization of AvBD2 in the mucosa with high individual variability, without showing differences attributable to quality indicators, but interestingly showing inverse correlation with seric IgM levels in the fast-growing line. The availability of our anti-AvBD2 antibodies to the scientific community opens perspectives to identify the cellular sources of this defensin in the cecal mucosa and to investigate the organization and function of innate immune arsenal of birds.

Lactobacillus acidophilus and Bacillus subtilis significantly change the growth performance, serum immunity and cecal microbiota of Cherry Valley ducks during the fattening period

This study explored the effects of a Bacillus subtilis and Lactobacillus acidophilus mixture containing the co-fermented products of the two probiotics on growth performance, serum immunity and cecal microbiota of Cherry Valley ducks. This study included 480 one-day-old Cherry Valley ducks divided into four feeding groups: basal diet (control group) and basal diet supplemented with 300, 500, or 700 mg/kg of the probiotic powder; the ducks were raised for 42 days. Compared with the control group, body weight on day 42 and the average daily gain on days 15-42 significantly increased (p < 0.05), and the feed conversion rate significantly decreased (p < 0.05) in the experimental groups. Furthermore, the serum immunoglobulin (Ig) A, IgG, IgM, and interleukin (IL)-4 levels increased significantly (p < 0.05), and IL-1β, IL-2, and tumor necrosis factor-α decreased significantly (p < 0.05) in the experimental groups. Finally, Sellimonas, Prevotellaceae NK3B31 group, Lachnospiraceae NK4A136 group and Butyricoccus played an important role in the cecal microbiota of the experimental group. Thus, the probiotic powder has impacts on the growth performance, serum immunity and cecal microbiota of Cherry Valley Ducks.

Integrated multi-omics reveals the roles of cecal microbiota and its derived bacterial consortium in promoting chicken growth

IMPORTANCE

The improvement of chicken growth performance is one of the major concerns for the poultry industry. Gut microbes are increasingly evidenced to be associated with chicken physiology and metabolism, thereby influencing chicken growth and development. Here, through integrated multi-omics analyses, we showed that chickens from the same line differing in their body weight were very different in their gut microbiota structure and host-microbiota crosstalk; microbes in high body weight (HBW) chickens contributed to chicken growth by regulating the gut function and homeostasis. We also verified that a specific bacterial consortium consisting of isolates from the HBW chickens has the potential to be used as chicken growth promoters. These findings provide new insights into the potential links between gut microbiota and chicken phenotypes, shedding light on future manipulation of chicken gut microbiota to improve chicken growth performance.

Comparison of yeast-derived commercial feed additives on Salmonella Enteritidis survival and microbiota populations in rooster cecal in vitro incubations

Yeast-derived products have become more of an interest in the poultry industry as of late because of their use in modulating the gastrointestinal tract (GIT) microbiome to both improve production parameters and prevent infection. This study aimed to evaluate the effects of various yeast-derived products on Salmonella enterica inoculation in un in vitro rooster cecal incubations and associated effects on the cecal microbiome. Cecal contents were obtained from 53-wk old White Leghorn H & N Nick Chick roosters (n = 3) fed a wheat-based, commercial-type basal diet. Cecal contents were diluted 1:3000 in anaerobic dilution solution (ADS) in an anaerobic chamber, with 20 mL aliquoted to each serum bottle. There were three controls (n = 3): basal diet only, diluted cecal contents only, and basal diet and diluted cecal contents; and five treatments containing the basal diet and diluted cecal contents (n = 3): Citristim® (ADM), ImmunoWall® (ICC), Maxi-Gen Plus® (CBS Bio Platforms), Hilyses® (ICC), and Original XPC® (Diamond V). All treatments were applied at a rate of 2.5 kg/tonne or less. All groups were inoculated with a nalidixic acid-resistant strain of Salmonella Enteritidis at 10^7 CFU/mL and incubated at 37 deg C. Samples were collected at 0, 24, and 48 h for S. Enteritidis enumeration and 16S rDNA microbial sequencing. Salmonella data were log-transformed and analyzed in a two-way ANOVA with means separated using Tukey's HSD (P≤0.05). Genomic DNA was extracted, and resulting libraries were prepared and sequenced using an Illumina MiSeq. Sequencing data were analyzed in QIIME2 (2021.4) with diversity metrics (alpha and beta), and an analysis of the composition of microbiomes (ANCOM) was performed. Main effects were considered significant at P≤0.05, with pairwise differences considered significant at Q≤0.05. There was an interaction of treatment and time on the enumeration of Salmonella where treatments of Citristim, Immunowall, Hilyses, and XPC reduced Salmonella by 1 log CFU/mL compared to the controls. At 48 h, each yeast product treatment reduced Salmonella by 3 log CFU/mL compared to the controls. There was no main effect of treatment on the alpha diversity metrics, richness, or evenness (P > 0.05). Treatment affected the beta diversity, abundance, and phylogenetic differences, but there were no pairwise differences (P>0.05, Q>0.05). Using ANCOM at the genus level, the taxa Synergistes, Alloprevotella, Sutterella, and Megasphaera abundance were significantly different (W = 154,147,145,140, respectively). These results demonstrate the potential of these yeast-derived products to reduce foodborne pathogens, such as Salmonella Enteriditis, in vitro, without negatively disrupting the cecal microbiome.

Research Note: The effects of a Lactobacillus helveticus ATCC 15009-derived postbiotic mitigating Salmonella Gallinarum colonization in commercial layer chicks

This study aimed to assess the effects of a Lactobacillus helveticus ATCC 15009-derived postbiotic in mitigating experimental Salmonella Gallinarum infection. For this purpose, a sample of Lactobacillus sp. was inoculated in 2 different media, each containing different postbiotics (sensitized and nonsensitized). Both inocula had their antagonistic effect over S. Gallinarum tested through the spot-on-the-lawn method. It revealed that the sensitized postbiotic had a higher action potential over Lactobacillus sp. than the nonsensitized one (P < 0.05). Then, 48 day of hatch chicks were divided into 4 groups: A = Lactobacillus sp. (109 CFU/mL) inoculum on the 18th day; B = Lactobacillus sp. (109 CFU/mL) inoculum on the 18th day and postbiotic inoculum on the 19th day; C = postbiotic inoculum on the 19th day; and D = sterile saline inoculum on 18th and 19th days. On the 21st day, all chicks were infected with S. Gallinarum (109 CFU/mL). On the 23rd day, the animals were euthanized by cervical dislocation, and the ceca and liver were aseptically removed. Bacterial count of S. Gallinarum with serial decimal dilution was performed with these organs. It revealed that the prophylactic treatment with the postbiotic that modulates the intestinal microbiota was as efficient as the probiotic administration in reducing S. Gallinarum in the cecum and liver of chicks (P < 0.05). These data point to a new range of alternatives for preventing S. Gallinarum, which might help the poultry industry produce safer food for human consumption.

Regulating effects of chlorinated drinking water on cecal microbiota of broiler chicks

In this study, 2 types of drinking water were provided to broiler chicks to evaluate the relationship between the bacterial load of drinking water and cecal microbiota. One type of drinking water was untreated, while the other type was daily treated with sodium dichlorocyanurate (50 mg/L). A total of 240 broiler chicks were divided into 2 groups based on their initial body weight. There were 6 replicates in each group, and each replicate cage contained 20 birds. Each cage was assigned to a different floor of the battery cage. On the final day, water samples were collected from each replicate cage at the opening of the drinking cup height, and one bird was selected from each replicate cage to obtain cecal content samples for measuring microbiota composition using the 16S rRNA technique. We found that drinking water treated with sodium dichlorocyanurate significantly reduced the richness and diversity of microbiota and diminished/disappeared most gram-negative bacteria. Broiler chicks that consumed chlorinated drinking water exhibited changes in the composition of cecal microbiota, with Alistipes serving as the marker species in the cecal content of broiler chicks that consumed untreated water, whereas AF12 served as the marker species in the cecal content of broiler chicks that consumed chlorinated drinking water. Functional prediction using the MetaCyc database and species composition analysis of metabolic pathways showed that changes in 7 metabolic pathways were related to the abundance of Providencia. Therefore, we concluded that chlorinated drinking water reduced the bacterial load in drinking water, thereby altering the cecal microbiota composition and regulating the metabolic activity of broiler chicks.

Metabolomic and microbiome analysis of the protective effects of Puerarin against Salmonella Enteritidis Infection in chicks

BACKGROUND

Salmonella Enteritidis is a zoonotic pathogen and poses a substantial risk to human health, as well as significant financial losses to the livestock and poultry industries. It is currently urgent to identify alternatives to antibiotic treatment.

RESULTS

In this study, we explored the influence of Puerarin on the immunological response, intestinal flora, serum metabolome, and growth performance of chicks infected with Salmonella Enteritidis. Chicks were weighed at specific time points and the average daily gain (ADG) was calculated. Serum, intestinal, and cecal content samples were collected on days 10 and 17. The results showed that 100 mg/kg of Puerarin significantly suppressed inflammation and enhanced immune function. Metabolomic analysis showed significant differences in serum metabolites after Puerarin treatment and suggested that Puerarin may regulate abnormal amino acid and lipid metabolism after Salmonella Enteritidis infection through the autophagic and ABC transporter pathways. In addition, Puerarin suppressed Salmonella Enteritidis-induced intestinal flora dysbiosis through modulation of the microbial community structures (increased Lactobacillus, Faecalibacterium, and Subdoligranulum), as demonstrated by 16S rRNA analysis.

CONCLUSIONS

In conclusion, Puerarin can improve growth performance in chicks, suppress the inflammatory response in vivo, enhance immunity, and regulate lipid and amino acid metabolism and the intestinal flora.

Gut microbiota disruption during sepsis and the influence of innate metabolites on sepsis prognosis

Sepsis causes high mortality in intensive care units. Although there have been many studies on the gut microbiota in patients with sepsis, the impact of sepsis on the gut microbiota has not been directly determined because the treatment of sepsis also affects the gut microbiota. Therefore, we designed this animal experiment to explore gut microbiota alterations during sepsis. Mice were divided into two groups, mice that survived less than 3 days and mice that survived more than 3 days. Fecal samples collected on the day of cecal ligation and puncture (CLP), as well as on the 3rd and 7th days after CLP, were subjected to microbial community analysis and nontargeted metabolomics analysis. The results showed significantly lower bacterial diversity in fecal samples after CLP. At the genus level, the fecal samples obtained on the 3rd and 7th days after CLP exhibited significantly increased relative abundances of Bacteroides, Helicobacter, etc., and significantly decreased relative abundances of Alloprevotella, Prevotella, etc. Innate metabolite levels were significantly different in mice that survived less than 3 days and mice that survived more than 3 days. In conclusion, CLP-induced sepsis in mice changes the structure of the gut microbiome, and innate metabolites affect the prognosis of septic mice.

Enterococcus faecium supplementation prevents enteritis caused by Escherichia coli in goats

The probiotic Enterococcus faecium is a gut microbe with immunomodulatory effects, which has been widely used to prevent diarrhoea in pigs and birds. Escherichia coli is a common pathogen that causes inflammatory bowel disease in animals. The aim of this study was to investigate the protective effects of E. faecium on enteritis in goats. Forty goats were randomly divided into 4 treatment groups: control, E. faecium, E. coli, and E. faecium + E. coli. The changes of physiological indicators and diarrhoea scoring were evaluated on days -4, -2, 0, 2, 4, 6, and 8. The pathological examination, inflammatory cytokines mRNA expression and bacterial counts in jejunum and caecum were detected on day 4 and 8. The results showed that body temperature, respiratory rate, heart rate and leukocyte counts all increased from the 2nd to the 6th day after feeding with E. coli, and the diarrhoea score was significantly increased. However, E. faecium-pretreated goats had lower body temperatures and fewer leukocytes than E. coli-treated goats on day 2, as well as decreased diarrhoea scores. E. coli treatment caused histopathological damage and morphological changes in the jejunum and caecum, while pretreatment with E. faecium significantly alleviated these injuries. E. faecium pretreatment can reduce the load of E. coli and increase the prevalence of Lactobacillus, thereby balancing the microbiota in the intestine. Furthermore, E. coli-infected goats pretreated with E. faecium showed obvious inhibition of Toll-like receptor 4, interleukin (IL)-1β, IL-6, IL-8 and tumour necrosis factor-α mRNA expression in the jejunum and caecum compared to that in the E. coli treatment group. In conclusion, the addition of E. faecium to goat feed is beneficial for improving clinical symptoms, maintaining intestinal mucosa integrity, balancing the microbiota and decreasing inflammatory responses in E. coli-induced intestinal injury.

Modulation of Caecal Microbiota and Metabolome Profile in Salmonella-Infected Broilers by Phage Therapy

Bacteriophage therapy is considered one of the most promising tools to control zoonotic bacteria, such as Salmonella, in broiler production. Phages exhibit high specificity for their targeted bacterial hosts, causing minimal disruption to the niche microbiota. However, data on the gut environment's response to phage therapy in poultry are limited. This study investigated the influence of Salmonella phage on host physiology through caecal microbiota and metabolome modulation using high-throughput 16S rRNA gene sequencing and an untargeted metabolomics approach. We employed 24 caecum content samples and 24 blood serum samples from 4-, 5- and 6-week-old broilers from a previous study where Salmonella phages were administered via feed in Salmonella-infected broilers, which were individually weighed weekly. Phage therapy did not affect the alpha or beta diversity of the microbiota. Specifically, we observed changes in the relative abundance of 14 out of the 110 genera using the PLS-DA and Bayes approaches. On the other hand, we noted changes in the caecal metabolites (63 up-accumulated and 37 down-accumulated out of the 1113 caecal metabolites). Nevertheless, the minimal changes in blood serum suggest a non-significant physiological response. The application of Salmonella phages under production conditions modulates the caecal microbiome and metabolome profiles in broilers without impacting the host physiology in terms of growth performance.

The digestive tract histology and geographical distribution of gastrointestinal microbiota in yellow-feather broilers

Exhaustive understanding of intestinal physiological characteristics is the critical precondition for the improvement of intestinal health and growth performance of yellow-feather broilers (YFB). As a vital part of gastrointestinal tract, the symbiotic, complex, and variable microbiota have a profound effect on the nutrition, immunity, health, and production of broilers. Hence, the development status of proventriculus, jejunum, and cecum, and spatial heterogeneity of bacterial community in crop, proventriculus, gizzard, jejunum, cecum, and rectum of adult YFB were detected in our study. The results revealed that proventriculus, jejunum, and cecum of broilers are well-developed based on morphological observation. The Chao and Shannon indexes in cecum and rectum are notably higher than other sections and their microbiota structure is also distinct from foregut. Firmicutes and Lactobacillus are the predominant phylum and genus in all gastrointestinal sections, respectively. As feature species of crop, Lactobacillus spp. mainly settle in foregut, whereas some Clostridia species (unclassified Lachnospiraceae, Faecalibacterium, Romboutsia and so on) are characteristic and more abundant in cecum and rectum. Interestingly, there are 2 Ruminococcus torques strains positively and negatively correlated with cecum development, respectively. In a whole, our findings reveal the specialized digestive physiology and regional distribution of intestinal microbiota in YFB, which provides a reference for the future study on the improvement of growth performance and intestinal development through microbiota manipulation in yellow-feather broilers.

Microbiota-Dependent Upregulation of Bitter Taste Receptor Subtypes in the Mouse Large Intestine in High-Fat Diet-Induced Obesity

Bitter taste receptors (Tas2rs in mice) detect bitterness, a warning signal for toxins and poisons, and are expressed in enteroendocrine cells. We tested the hypothesis that Tas2r138 and Tas2r116 mRNAs are modulated by microbiota alterations induced by a long-term high-fat diet (HFD) and antibiotics (ABX) (ampicillin and neomycin) administered in drinking water. Cecum and colon specimens and luminal contents were collected from C57BL/6 female and male mice for qRT-PCR and microbial luminal 16S sequencing. HFD with/without ABX significantly increased body weight and fat mass at 4, 6, and 8 weeks. Tas2r138 and Tas2r116 mRNAs were significantly increased in mice fed HFD for 8 weeks vs. normal diet, and this increase was prevented by ABX. There was a distinct microbiota separation in each experimental group and significant changes in the composition and diversity of microbiome in mice fed a HFD with/without ABX. Tas2r mRNA expression in HFD was associated with several genera, particularly with Akkermansia, a Gram-negative mucus-resident bacterium. These studies indicate that luminal bacterial composition is affected by sex, diet, and ABX and support a microbial dependent upregulation of Tas2rs in HFD-induced obesity, suggesting an adaptive host response to specific diet-induced dysbiosis.

Extremely hair follicle density is associated with a significantly different cecal microbiota in rex rabbits

It has become increasingly clear that gut microbiota and skin are interconnected since the discovery of the 'gut-brain-skin' axis. Hair follicles (HFs) are skin microorganisms, but few studies have investigated their relationship to gut microbiota. Hence, we hypothesize that HFs have a close relationship with the gut, similarly to what was reported for the skin. Using rex rabbits as an animal model, one hundred healthy half-sibling rex rabbits were selected for the experiment, and 16 s rRNA gene sequencing was performed on the cecal microbiota of nine rabbits with the extremely high (HS) and low (LS) hair density (n = 9 per group) to determine differences between the composition and function of these communities. In comparison with the LS group, several alpha diversity index values were significantly lower in the HS group, although the higher variation in species composition in the HS group. Additionally, species diversity and abundance differed significantly in the cecum microbiota of HS and LS rabbits. Further, primary and secondary HF density was significantly correlated with the families Muribaculaceae and Bacteroidaceae, and genera Blautia, Bacteroides and Desulfovibrio. In particular, Muribaculaceae, Bacteroidaceae, Blautia and Bacteroides may support the development of HFs. Moreover, the expression of WNT4, WNT10a, WNT10b, CTNNB1 (β-catenin) and LEF1 in the skin was significantly higher in the HS group compared with the LS group. Altogether, the results of this study suggest that the extremely high density of HF in rabbits is associated with a significantly different microbiota diversity and community structure, and the Wnt/β-catenin signalling pathway was activated in the HS group. Thus, key bacteria may promote the development of HF.

Effects of grape seed procyanidins on antioxidant function, barrier function, microbial community, and metabolites of cecum in geese

The gut is the first line of defense for body health and is essential to the overall health of geese. Grape seed procyanidins (GSPs) are proverbial for their antioxidant, anti-inflammatory, and microflora-regulating capabilities. This study aimed to inquire into the influences of dietary GSPs on the intestinal antioxidant function, barrier function, microflora, and metabolites of geese based on 16S rRNA sequencing and metabolomics. In total, 240 twenty-one-day-old Sichuan white geese were randomly divided into 4 groups, each of which was supplied with 1 of 4 diets: basal diet or a basal diet supplemented with 50, 100, or 150 mg/kg GSPs. Diets supplemented with GSPs at different concentrations significantly increased the total antioxidant capacity and superoxide dismutase activity in cecal mucosa (P < 0.001). Dietary supplementation with 50 or 100 mg/kg GSPs significantly increased catalase activity (P < 0.001). The serum diamine oxidase, D-lactic acid, and endotoxin concentrations were decreased by GSP supplementation in the goose diet. Dietary GSP supplementation increased microbial richness and diversity, enhanced the relative abundance of Firmicutes, and decreased that of Bacteroidetes in the cecum. Diets supplemented with 50 or 100 mg/kg GSPs enriched Eubacterium coprostanoligenes and Faecalibacterium. Dietary GSPs substantially raised the acetic and propionic acid concentrations in the cecum. The butyric acid concentration increased when the GSP dosage was 50 or 100 mg/kg. Additionally, dietary GSPs increased the levels of metabolites that belong to lipids and lipid-like molecules or organic acids and derivatives. Dietary GSP supplementation at 100 or 150 mg/kg reduced the levels of spermine (a source of cytotoxic metabolites) and N-acetylputrescine, which promotes in-vivo inflammation. In conclusion, dietary supplementation with GSPs was beneficial to gut health in geese. Dietary GSPs improved antioxidant activity; protected intestinal barrier integrity; increased the abundance and diversity of cecal microflora; promoted the proliferation of some beneficial bacteria; increased the production of acetic, propionic, and butyric acids in the cecum; and downregulated metabolites associated with cytotoxicity and inflammation. These results offer a strategy for promoting intestinal health in farmed geese.

Age-associated changes in the growth development of abdominal fat and their correlations with cecal gut microbiota in broiler chickens

Excess abdominal fat is a common phenomenon in broiler chickens. Gut microbiota could regulate lipid metabolism through their effects on short-chain fatty acids (SCFAs) production. This study was conducted to investigate the potential relationship between abdominal fat development and cecal microorganism populations. Abdominal fat and cecum contents were collected at 3, 7, 14, 21, 28, 35, and 42 d of age. The results showed that abdominal fat weight increased with age. The abdominal fat percentage was higher between 7 and 21 d of age than at 3 d (P < 0.05), and it increased again at 28 to 42 d (P < 0.05). Morphological analysis showed that adipocyte diameter and cross-sectional area (CSA) increased significantly after 14 d of age (P < 0.05). Moreover, gut microbiota analysis indicated that the Chao1 and Shannon indices were higher between 14 and 28 d than at 3 d of age (P < 0.05). Furthermore, LEfse analysis revealed that Faecalibacterium, Anaerotruncus, Anaeroplasma, Subdoligranulum, and Clostridium emerged to become dominant at 14 d. A greater abundance of Bacteroides, Ruminococcus, Dehalobacterium, and Lactobacillus were determined at 28 d when compared with 14 d of age. Parabacteroides, Ochrobactrum, Lactobacillus, Blautia, Alistipes, Dehalobacterium, Odoribacter, and Suuterella were found to be predominant at 42 d. PICRUSt analysis revealed that amino acid metabolism, lipid metabolism, and terpenoids and polyketides metabolism were elevated at 14 d; the immune and digestive systems were significantly developed at 28 d. In addition, cecum propionic acid and butyric acid contents gradually increased (P < 0.05), while the isobutyric acid contents gradually decreased with advancing age (P < 0.05). Correlation analysis among SCFAs, differential genera and abdominal fat suggested that Coprobacillus, Shigella, and Butyricicoccus had negative correlations with propionic acid, butyric acid, and abdominal fat weight, but positive correlations with isobutyric acid. Isobutyric acid was identified as being negatively associated with abdominal fat weight, while the reverse was found for propionic acid and butyric acid. In conclusion, abdominal fat development is correlated with the emergence of specific microbes and d 14 may be a pivotal age for establishing this relationship.

Impact of different dietary fibre sources on production performance, bacterial composition and metabolites in the caecal contents of rabbits

This study was conducted to investigate the effects of different dietary fibre sources on growth performance, gastrointestinal tract development, caecal fermentation and bacterial composition in the caecal contents of rabbits. A total of 120 35-day-old weaned Minxinan black rabbits were divided into three groups and fed a diet composed of peanut straw powder (Group A), alfalfa powder (Group B) and soybean straw powder (Group C) as the main fibre source. The final body weight and average daily gain in Group B were higher than those in Group C, and the average daily feed intake and feed conversion ratio in Group A were lower than those in Group C (p < 0.05). The relative weights of the stomach, small intestine and caecum of rabbits in Group C were higher than those in Groups of B and A, and the relative weights of the caecal contents in Group C were lower than those in Groups A or B (p < 0.05). The pH value and propionic acid, butyric acid and valeric acid concentrations in the caecum of Group C were lower than those in the caecum of Groups A or B, and the concentration of acetic acid in the caecum was lower (p < 0.05). The dominant microbes in the caecal contents of Minxinan black rabbits were Firmicutes, Bacteroidetes and Proteobacteria at the phylum level, and the number of species, Chao1 index and ACE index measured was different between the B-C and A-C groups (p < 0.05). Different dietary fibre sources could affect the growth performance, gastrointestinal tract development and intestinal microbiota of rabbits, and the nutritional value of alfalfa powder was better than that of peanut straw and soybean straw.

Characterizing the gut microbiome of broilers raised under conventional and no antibiotics ever practices

Meat from broilers raised without the use of antibiotics is becoming increasingly popular among consumers. Consequently, interest in the microbial profiling of chickens produced under nonconventional practices is growing, however, research on this topic is lacking. The current study was designed to characterize the dynamics of gut microbial populations of broilers raised under conventional and no antibiotics ever (NAE) practices. Four commercial farms (2 conventional and 2 NAE) were included in this study. On each farm, cecal (n = 224) and ileal (n = 224) contents were collected from birds at different stages during the grow out of a single flock and following transportation to the processing facility. Cecal microbiota was dominated by the genera Escherichia and Enterococcus upon hatching in both conventional and NAE flocks, shifting with time toward predominantly Faecalibacterium and Bacteroides. The composition of cecal microbial communities of NAE broilers was different than that of conventional chickens (P ≤ 0.05). Conventional broilers harbored a rich, but less diverse cecal microbiota than NAE, while the ileal microbiota was primarily populated with genera previously named Lactobacillus, which exhibited a higher abundance in NAE broilers (P ≤ 0.05). In both production systems, the microbiota followed a similar temporal succession that was more evident in the ceca. Transportation to the processing plant impacted the microbial composition of the ileum (P ≤ 0.05), characterized by an increase in the relative abundance of Psychrobacter. Finally, differential abundance analysis showed a positive correlation between Campylobacter and Enorma within the cecum microbiota, and a negative correlation with Salmonella.

Cecal Microbiota Development and Physiological Responses of Broilers Following Early Life Microbial Inoculation Using Different Delivery Methods and Microbial Sources

Broilers in intensive systems may lack commensal microbes that have coevolved with chickens in nature. This study evaluated the effects of microbial inocula and delivery methods applied to day-old chicks on the development of the cecal microbiota. Specifically, chicks were inoculated with cecal contents or microbial cultures, and the efficacies of three delivery methods (oral gavage, spraying inoculum into the bedding, and cohousing) were evaluated. Also, a competitive study evaluated the colonization ability of bacteria sourced from extensive or intensive poultry production systems. The microbiota of inoculated birds presented higher phylogenetic diversity values (PD) and higher relative abundance values of Bacteroidetes, compared with a control. Additionally, a reduction in the ileal villus height/crypt depth ratio and increased cecal IL-6, IL-10, propionate, and valerate concentrations were observed in birds that were inoculated with cecal contents. Across the experiments, the chicks in the control groups presented higher relative abundance values of Escherichia/Shigella than did the inoculated birds. Specific microbes from intensively or extensively raised chickens were able to colonize the ceca, and inocula from intensive production systems promoted higher relative abundance values of Escherichia/Shigella. We concluded that Alistipes, Bacteroides, Barnesiella, Mediterranea, Parabacteroides, Megamonas, and Phascolarctobacterium are effective colonizers of the broiler ceca. In addition, oral gavage, spray, and cohousing can be used as delivery methods for microbial transplantation, as indicated by their effects on the cecal microbiota, intestinal morphology, short-chain fatty acids concentration, and cytokine/chemokine levels. These findings will guide future research on the development of next-generation probiotics that are able to colonize and persist in the chicken intestinal tract after a single exposure. IMPORTANCE The strict biosecurity procedures employed in the poultry industry may inadvertently hinder the transmission of beneficial commensal bacteria that chickens would encounter in natural environments. This research aims at identifying bacteria that can colonize and persist in the chicken gut after a single exposure. We evaluated different microbial inocula that were obtained from healthy adult chicken donors as well as three delivery methods for their effects on microbiota composition and bird physiology. In addition, we conducted a competitive assay to test the colonization abilities of bacteria sourced from intensively versus extensively raised chickens. Our results indicated that some bacteria are consistently increased in birds that are exposed to microbial inoculations. These bacteria can be isolated and employed in future research on the development of next-generation probiotics that contain species that are highly adapted to the chicken gut.

Effects of citrus pulp on the composition and diversity of broiler cecal microbes

Diet may affect gut microbial composition and diversity. There were 3 dietary groups: 0% citrus pulp diet (C), 1.5% citrus pulp diet (I), and 2.5% citrus pulp diet (II). A total of 180 healthy AA broilers (21-day old) were divided into 3 groups (C, I, and II), each group was set up with 6 replicates, and each replicate including 10 broilers (half male and female). At 42 d, the cecal contents of 18 broiler chickens were collected after slaughter. The cecal contents were analyzed using 16S rRNA sequencing technology. Compared with group C, the abundance of Firmicutes in groups I and II decreased, while the relative abundances of Bacteroidetes, Verrucomicrobia, Lactobacillus, and Faecalibacterium increased. LEfSe analysis showed that Actinobacteria, Coriobacteriia, Coriobacteriales, and Ruminococcaceae_bacterium_Marseille_P2935 in group I were significantly higher than those in group C. Bacteria, Coriobacteriales, Coriobacteriia, Coriobacteriaceae, Slackia, Bacteroides_sp_Marseille_P3132, and Lactobacillus_pontis in group II were significantly higher than those in group C. The Staphylococcaceae, Bacteroides_sp_Marseille_P3132, Macroccus, Lactobacillus_pontis, and Streptococcus_equinus in group II were significantly higher than those in group I. Functional predictions indicated that the cecal microbiota of broilers fed the 2.5% citrus pulp diet was more tend to utilize carbohydrates through glycolytic/gluconeogenesis metabolism. Adding citrus pulp to the diet affects the microbial composition and has important implications for studying gut health and improving economic benefits.

Taxonomic and Metagenomic Analyses Define the Development of the Microbiota in the Chick

Chicks are ideal to follow the development of the intestinal microbiota and to understand how a pathogen perturbs this developing population. Taxonomic/metagenomic analyses captured the development of the chick microbiota in unperturbed chicks and in chicks infected with Salmonella enterica serotype Typhimurium (STm) during development. Taxonomic analysis suggests that colonization by the chicken microbiota takes place in several waves. The cecal microbiota stabilizes at day 12 posthatch with prominent Gammaproteobacteria and Clostridiales. Introduction of S. Typhimurium at day 4 posthatch disrupted the expected waves of intestinal colonization. Taxonomic and metagenomic shotgun sequencing analyses allowed us to identify species present in uninfected chicks. Untargeted metabolomics suggested different metabolic activities in infected chick microbiota. This analysis and gas chromatography-mass spectrometry on ingesta confirmed that lactic acid in cecal content coincides with the stable presence of enterococci in STm-infected chicks. Unique metabolites, including 2-isopropylmalic acid, an intermediate in the biosynthesis of leucine, were present only in the cecal content of STm-infected chicks. The metagenomic data suggested that the microbiota in STm-infected chicks contained a higher abundance of genes, from STm itself, involved in branched-chain amino acid synthesis. We generated an ilvC deletion mutant (STM3909) encoding ketol-acid-reductoisomerase, a gene required for the production of l-isoleucine and l-valine. ΔilvC mutants are disadvantaged for growth during competitive infection with the wild type. Providing the ilvC gene in trans restored the growth of the ΔilvC mutant. Our integrative approach identified biochemical pathways used by STm to establish a colonization niche in the chick intestine during development. IMPORTANCE Chicks are an ideal model to follow the development of the intestinal microbiota and to understand how a pathogen perturbs this developing population. Using taxonomic and metagenomic analyses, we captured the development of chick microbiota to 19 days posthatch in unperturbed chicks and in chicks infected with Salmonella enterica serotype Typhimurium (STm). We show that normal development of the microbiota takes place in waves and is altered in the presence of a pathogen. Metagenomics and metabolomics suggested that branched-chain amino acid biosynthesis is especially important for Salmonella growth in the infected chick intestine. Salmonella mutants unable to make l-isoleucine and l-valine colonize the chick intestine poorly. Restoration of the pathway for biosynthesis of these amino acids restored the colonizing ability of Salmonella. Integration of multiple analyses allowed us to correctly identify biochemical pathways used by Salmonella to establish a niche for colonization in the chick intestine during development.

Dietary benzoic acid and supplemental enzymes alter fiber-fermenting taxa and metabolites in the cecum of weaned pigs

Inclusion of enzymes and organic acids in pig diets is an important strategy supporting decreased antibiotic usage in pork production. However, limited knowledge exists about how these additives impact intestinal microbes and their metabolites. To examine the effects of benzoic acid and enzymes on gut microbiota and metabolome, 160 pigs were assigned to one of four diets 7 days after weaning: a control diet or the addition of 0.5% benzoic acid, 0.045% dietary enzymes (phytase, β-glucanase, xylanase, and α-amylase), or both and fed ad libitum for 21 to 22 d. Individual growth performance and group diarrhea incidence data were collected throughout the experimental period. A decrease of 20% in pen-level diarrhea incidence from days 8 to 14 in pigs-fed both benzoic acid and enzymes compared to the control diet (P = 0.047). Cecal digesta samples were collected at the end of the experimental period from 40 piglets (n = 10 per group) and evaluated for differences using 16S rRNA sequencing and two-dimensional gas chromatography and time-of-flight mass spectrometry (GCxGC-TOFMS). Analysis of cecal microbiota diversity revealed that benzoic acid altered microbiota composition (Unweighted Unifrac, P = 0.047, r2 = 0.07) and decreased α-diversity (Shannon, P = 0.041; Faith's Phylogenetic Diversity, P = 0.041). Dietary enzymes increased fiber-fermenting bacterial taxa such as Prevotellaceae. Two-step feature selection identified 17 cecal metabolites that differed among diets, including increased microbial cross-feeding product 1,2-propanediol in pigs-fed benzoic acid-containing diets. In conclusion, dietary benzoic acid and enzymes affected the gut microbiota and metabolome of weaned pigs and may support the health and resolution of postweaning diarrhea.

Influence of Eimeria maxima coccidia infection on gut microbiome diversity and composition of the jejunum and cecum of indigenous chicken

Coccidiosis is an economically significant protozoan disease and an intracellular parasite that significantly impacts poultry production. The gastrointestinal tract microbiota plays a central role in host health and metabolism, and these microbes enhance chickens’ immune systems and nutrient absorption. In this study, we analyzed the abundance and diversity of microbiota of the jejunum and cecum of a dual-purpose indigenous Horro chicken following Eimeria maxima infection. We compared microbial abundance, composition, and diversity at the 4- and 7- days post-infection using 16S rRNA gene sequencing. We obtained, on average, 147,742 and 132,986 high-quality sequences per sample for jejunum and cecum content, respectively. Firmicutes, Proteobacteria, Campilobacterota and Bacteroidota were the major microbial phylum detected in the jejunum content. Firmicutes were the dominant phylum for 4- and 7-days jejunum control groups accounting for (>60% of the sequences). In the infected group Campilobacterota was the dominant phylum in the jejunum (> 24% of sequences) at 4-and 7-days post-infection groups, while Proteobacteria was predominant at 4- and 7-days post-infection of the cecum (> 40% of the sequences). The microbial genus Lactobacillus and Helicobacter were found in the jejunum, while Alistipes, Barnesiella and Faecalibacterium were detected in the cecum. In the jejunum, Helicobacter was dominant at 4 -and-7 days post-infection (≥24%), and Lactobacillus was dominant at 4 -and 7- days in the control group (> 50%). In 4- and 7-days post-infection, Alistipes genus was the more prevalent (> 38%) in the cecum. Thus, clear differences were observed in the bacterial microbiota distribution and abundance between the jejunum and cecum, as well as between infected and control groups for both tissues. The results indicate that chicken intestinal microbial imbalance (dysbiosis) is associated with Eimeria parasite infection and will likely affect the host-microbial non-pathogenic and pathogenic molecular interactions.

Bacteroides muris sp. nov. isolated from the cecum of wild-derived house mice

Two bacterial strains, KH365_2^T and KH569_7, were isolated from the cecum contents of wild-derived house mice. The strains were characterized as Gram-negative, rod-shaped, strictly anaerobic, and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences revealed that both strains were most closely related to Bacteroides uniformis ATCC 8492^T. Whole genome sequences of KH365_2^T and KH569_7 strains have a DNA G + C content of 46.02% and 46.03% mol, respectively. Most morphological and biochemical characteristics did not differ between the newly isolated strains and classified Bacteroides strains. However, the average nucleotide identity (ANI) and dDNA–DNA hybridization (dDDH) values clearly distinguished the two strains from described members of the genus Bacteroides. Here, we present the phylogeny, morphology, and physiology of a novel species of the genus Bacteroides and propose the name Bacteroides muris sp. nov., with KH365_2^T (DSM 114231^T = CCUG 76277^T) as type strain.

Effects of Different Monochromatic Light Combinations on Cecal Microbiota Composition and Cecal Tonsil T Lymphocyte Proliferation

Emerging data demonstrated that the gut microbiota plays an important role in protecting the integrity of the epithelial barrier, forming a mucosal immune system, and maintaining intestinal homeostasis through its metabolites. However, the intestinal microbiota community can be affected by environmental factors, such as litter, photoperiod, or temperature. Thus, we investigated the effect of different monochromatic light combinations on cecal microbiota composition as well as explored the molecular mechanism by how the external light color information mediate cecal tonsil T lymphocyte proliferation. In this study, a total of 160 chicks were exposed to monochromatic light [red (R), green (G), blue (B), or white (W) light] or green and blue monochromatic light combination (G→B) from P0 to P42. The 16S rRNA microbial sequencing results showed that the richness and diversity of the cecum microbiota and the abundance of Faecalibacterium and Butyricicoccus were significantly increased in the G→B. With consistency in the upregulation of antioxidant enzyme ability and downregulation of pro-inflammation levels in the cecum, we observed an increase in the number of goblet cells, secretory IgA+ cells, tight junction protein (occludin, ZO-1, and claudin-1) and MUC-2 expression in the cecum of the G→B. The metabolomics analysis revealed that the relative abundance of metabolites related to butyrate was significantly increased in G→B. In an in vitro experiment, we found that butyrate could effectively induce T lymphocyte proliferation and cyclin D1 protein expression. However, these butyrate responses were abrogated by HDAC3 agonists, STAT3 antagonists, or mTOR antagonists but were mimicked by GPR43 agonists or HDAC3 antagonists. Thus, we suggested that G→B can indirectly affect the composition of cecal microbiota as well as increase the relative abundance of Faecalibacterium and Butyricicoccus and butyrate production by reducing the level of oxidative stress in the cecum. Exogenous butyrate could promote the T lymphocyte proliferation of cecal tonsil by activating the GPR43/HDAC3/p-STAT3/mTOR pathways.

Identification of Nordic Berries with Beneficial Effects on Cognitive Outcomes and Gut Microbiota in High-Fat-Fed Middle-Aged C57BL/6J Mice

High-fat diets are associated with neuronal and memory dysfunction. Berries may be useful in improving age-related memory deficits in humans, as well as in mice receiving high-fat diets. Emerging research has also demonstrated that brain health and cognitive function may be related to the dynamic changes in the gut microbiota. In this study, the impact of Nordic berries on the brain and the gut microbiota was investigated in middle-aged C57BL/6J mice. The mice were fed high-fat diets (60%E fat) supplemented with freeze-dried powder (6% dwb) of bilberry, lingonberry, cloudberry, blueberry, blackcurrant, and sea buckthorn for 4 months. The results suggest that supplementation with bilberry, blackcurrant, blueberry, lingonberry, and (to some extent) cloudberry has beneficial effects on spatial cognition, as seen by the enhanced performance following the T-maze alternation test, as well as a greater proportion of DCX-expressing cells with prolongation in hippocampus. Furthermore, the proportion of the mucosa-associated symbiotic bacteria Akkermansia muciniphila increased by 4-14 times in the cecal microbiota of mice fed diets supplemented with lingonberry, bilberry, sea buckthorn, and blueberry. These findings demonstrate the potential of Nordic berries to preserve memory and cognitive function, and to induce alterations of the gut microbiota composition.

Chicken-Specific Kinome Analysis of Early Host Immune Signaling Pathways in the Cecum of Newly Hatched Chickens Infected With Salmonella enterica Serovar Enteritidis

Poultry is a major source of human foodborne illness caused by broad host range Salmonella serovars (paratyphoid), and developing cost-effective, pre-harvest interventions to reduce these pathogens would be valuable to the industry and consumer. Host responses to infectious agents are often regulated through phosphorylation. However, proteomic mechanisms of Salmonella acute infection biology and host responses to the bacteria have been limited concentrating predominately on the genomic responses of the host to infection. Our recent development of chicken-specific peptide arrays for kinome analysis of host phosphorylation-based cellular signaling responses provided us with the opportunity to develop a more detailed understanding of the early (4-24 h post-infection) host-pathogen interactions during the initial colonization of the cecum by Salmonella. Using the chicken-specific kinomic immune peptide array, biological pathway analysis showed infection with S. Enteritidis increased signaling related to the innate immune response, relative to the non-infected control ceca. Notably, the acute innate immune signaling pathways were characterized by increased peptide phosphorylation (activation) of the Toll-like receptor and NOD-like receptor signaling pathways, the activation of the chemokine signaling pathway, and the activation of the apoptosis signaling pathways. In addition, Salmonella infection induced a dramatic alteration in the phosphorylation events of the JAK-STAT signaling pathway. Lastly, there is also significant activation of the T cell receptor signaling pathway demonstrating the initiation of the acquired immune response to Salmonella infection. Based on the individual phosphorylation events altered by the early Salmonella infection of the cecum, certain conclusions can be drawn: (1) Salmonella was recognized by both TLR and NOD receptors that initiated the innate immune response; (2) activation of the PPRs induced the production of chemokines CXCLi2 (IL-8) and cytokines IL-2, IL-6, IFN-α, and IFN-γ; (3) Salmonella infection targeted the JAK-STAT pathway as a means of evading the host response by targeting the dephosphorylation of JAK1 and TYK2 and STAT1,2,3,4, and 6; (4) apoptosis appears to be a host defense mechanism where the infection with Salmonella induced both the intrinsic and extrinsic apoptotic pathways; and (5) the T cell receptor signaling pathway activates the AP-1 and NF-κB transcription factor cascades, but not NFAT.

Research Note: IsomiRs of chicken miR-146b-5p are activated upon Salmonella enterica serovar Enteritidis infection

In order to enrich the knowledge of chicken transcriptomic response to Salmonella enterica serovar Enteritidis infection, 2-day-old chicks were orally inoculated with this bacteria (1.0 × 10⁸ cfu/mL), and then the cecum tissues of 3 days post-inoculation were utilized for RNA sequencing (6 replicates each for treatment group and control group). After analysis, we found a variety of inflammatory genes were triggered at the mRNA level upon infection. Notably, the expression profiles at the miRNA level and the isomiR level were heterogeneous. Certain isomiRs of chicken miR-146b-5p were significantly increased by more than 2 times compared to control (Padj < 0.05). Combining the bioinformatics prediction, transcriptome data and RT-qPCR results, we deduced that the isomiRs of chicken miR-146b-5p might act to sustain the RIG-I-like receptor signaling and type I interferon induction by repressing USP3 transcript. Our findings provide a new perspective on the regulatory function of miR-146b-5p and facilitate the study of isomiRs.

Dietary medium-chain 1-monoglycerides modulates the community and function of cecal microbiota of broilers

BACKGROUND

Medium-chain monoglycerides (MGs) are a group of 1-monoglycerides of medium-chain fatty acids with strong antibacterial activity, which may influence the gut microbiota in the diet of broilers. The present study evaluated the effects of mixed MGs on the community and function of gut microbiota in broilers. A total of 528 newly hatched male yellow feathered broiler chicks were weighed and randomly assigned into four groups, including a basal diet (CON), a basal diet containing 300 mg kg^-1 MG (MG300), 450 mg kg^-1 MG (MG450), or 600 mg kg^-1 MG (MG600).

RESULTS

The cecal acetic acid, propionic acid, butyric acid, isobutyric acid, isovaleric acid and total short-chain fatty acid of broilers in the MG-containing groups were notably increased compared with the CON group. Dietary MG selectively increased the relative abundance of Bifidobacteriaceae, Bacteroides and an unclassified genus of Lachnospiraceae family, but decreased the proportion of an unclassified genus of Barnesiellaceae and a norank genus of Flavobacteriaceae family in the cecum of broilers. Functional prediction revealed that MG supplementation enriched the microbial gene abundance of amino acid metabolism and carbohydrate metabolism, while depleted the gene abundance of fat metabolism and energy metabolism. Moreover, the modulation of gut microbiota by MG supplementation was closely correlated with the alteration of muscle amino acids.

CONCLUSION

Dietary MGs altered the gut microbiota community structure and metabolites, and modulated the gene abundance of microbial metabolism pathways in the cecum of broilers, which may further influence the growth performance, nutrient utilization and meat quality of the host. © 2021 Society of Chemical Industry.

Effects of cage versus floor rearing system on goose intestinal histomorphology and cecal microbial composition

Due to the demand for modern goose production and the pressure of environmental protection, the rearing systems of geese are changing from traditional waterside rearing to intensive rearing systems such as floor rearing (FR) and cage rearing (CR) systems. However, little is known about the effects of different rearing systems on goose intestinal functions and cecal microbial composition. Therefore, this study aimed to compare intestinal histomorphology and cecal microbial composition differences in geese reared under CR and FR at 270 d of age. Histomorphological analysis showed that the ileal villus height (VH) to crypt depth (CD) ratio was significantly greater in CR than in FR (P < 0.001). Taxonomic analysis showed that the dominant bacteria of cecal microorganisms in both rearing systems were roughly similar, with Bacteroidota, Firmicutes, Fusobacteriota, and Proteobacteria being the dominant phyla while Bacteroides, Fusobacterium, and uncultured_bacterium_o_Bacteroidales being the dominant genera. Differentially abundant taxa between CR and FR were also identified using Linear Discriminant Analysis Effect Size (LEfSe) analysis (P < 0.05, LDA score > 3.5). Megamonas and Anaerobiospirillum were significantly enriched in the CR group at the genus level, while uncultured_bacterium_f_Rikenellaceae and Sutterella were significantly enriched in the FR group. Notably, we found that the relative abundance of uncultured_bacterium_f_Rikenellaceae was significantly negatively correlated with the ileal VH and VH/CD (P < 0.05). The relative abundance of Megamonas and Anaerobiospirillum were significantly negatively correlated with abdominal fat weight and relative abdominal fat weight (P < 0.01), whereas that of Sutterella was significantly positively correlated with abdominal fat weight and relative abdominal fat weight (P < 0.01). Furthermore, PICRUSt2 analysis indicated that the lipid metabolism pathways of cecal microorganisms were lower enriched in CR than in FR. In conclusion, compared with FR, the CR significantly changed goose ileal histomorphological characteristics and cecal microbial composition, thereby affecting goose physiological functions and production performance.

Sources and levels of copper affect liver copper profile, intestinal morphology and cecal microbiota population of broiler chickens fed wheat-soybean meal diets

Super dosing copper (Cu) has long been used as an alternative to antibiotic growth-promoters in broiler chickens' diet to improve gut health. This study was designed to compare nutritional and growth-promoting levels of Cu hydroxychloride (CH) with CuSO4 on gut health bio-markers and liver mineral profile of broiler chickens. Ross 308 chicks (n = 864) were randomly assigned to eight treatments, as basal diet containing no supplemental Cu; the basal diet with 15 or 200 mg/kg Cu as CuSO4; or 15, 50, 100, 150 or 200 mg/kg Cu from CH. The highest liver Cu content was observed in birds fed the diets with 200 mg/kg CuSO4 (P < 0.01). Serum FITC-d concentration as the leaky gut marker, and liver malondialdehyde concentration were not affected. Copper level or source had no effect on cecal short chain fatty acid and the mRNA expression of five jejunal genes involved in gut integrity. Negative linear responses of Cu were observed on Lactobacillus (P = 0.032), Bacteroides (P = 0.033), and Enterobacteriaceae (P = 0.028) counts. The jejunal villus height increased in birds fed CH at 200 and 100 mg/kg (P < 0.05). Increasing Cu levels, linearly and quadratically (P < 0.001), increased Cu excretion.

The gut microbiota of chickens in a commercial farm treated with a Salmonella phage cocktail

The microbiota in broiler chicken intestines affects the animals' health, metabolism, and immunity both positively and negatively. Accordingly, it has a significant impact on animal productivity. Phages, host-specific parasites of bacterial cells, are a promising antimicrobial alternative that selectively target pathogens without disturbing the microbiota. The purpose of this study is to further characterize the commensal microbial community at production scale in broiler chickens treated with a Salmonella phage treatment. We evaluated the cecal microbiota of broilers reared in a commercial farming system where a phage cocktail against Salmonella, SalmoFree was supplied to animals. To do so, two field trials were conducted, incorporating three doses of phages in the broilers' drinking water. Our results showed that the core microbiome (taxa that were present in more than 50% of samples) contained species that are key to microbiota adaptation in the last stage of the production cycle. Among these, there are some important degraders of complex polysaccharides and producers of short chain fatty acids (SCFA) such as Eisenbergiella and Lachnoclostridium. The phage cocktail did not affect the normal development of the microbiota's structure. The addition of the phage cocktail resulted in a significant reduction in Campylobacter and an increase in Butyricimonas, Helicobacter and Rikenellaceae, which are common inhabitants in chicken gut with known negative and positive effects on their health and metabolism. Altogether, we consider that these results contribute valuable information to the implementation of large-scale phage therapy technologies.

NLRP6 Inflammasome Modulates Disease Progression in a Chronic-Plus-Binge Mouse Model of Alcoholic Liver Disease

A considerable percentage of the population is affected by alcoholic liver disease (ALD). It is characterized by inflammatory signals from the liver and other organs, such as the intestine. The NLR family pyrin domain containing 6 (NLRP6) inflammasome complex is one of the most important inflammatory mediators. The aim of this study was to evaluate a novel mouse model for ALD characterized by 8-week chronic-plus-binge ethanol administration and to investigate the role of NLRP6 inflammasome for intestinal homeostasis and ALD progression using Nlrp6-/- mice. We showed that chronic-plus-binge ethanol administration triggers hepatic steatosis, injury, and neutrophil infiltration. Furthermore, we discovered significant changes of intestinal microbial communities, including increased relative abundances of bacteria within the phyla Bacteroidota and Campilobacterota, as well as reduced Firmicutes. In this ALD model, inhibiting NLRP6 signaling had no effect on liver steatosis or damage, but had a minor impact on intestinal homeostasis via affecting intestinal epithelium function and gut microbiota. Surprisingly, Nlrp6 loss resulted in significantly decreased hepatic immune cell infiltration. As a result, our novel mouse model encompasses several aspects of human ALD, such as intestinal dysbiosis. Interfering with NLRP6 inflammasome activity reduced hepatic immune cell recruitment, indicating a disease-aggravating role of NLRP6 during ALD.

Saffron (Crocus sativus L.) Flower Water Extract Disrupts the Cecal Microbiome, Brush Border Membrane Functionality, and Morphology In Vivo (Gallus gallus)

Saffron (Crocus sativus L.) is known as the most expensive spice. C. sativus dried red stigmas, called threads, are used for culinary, cosmetic, and medicinal purposes. The rest of the flower is often discarded, but is now being used in teas, as coloring agents, and fodder. Previous studies have attributed antioxidant, anti-inflammatory, hepatoprotective, neuroprotective, anti-depressant, and anticancer properties to C. sativus floral bio-residues. The aim of this study is to assess C. sativus flower water extract (CFWE) for its effects on hemoglobin, brush boarder membrane (BBM) functionality, morphology, intestinal gene expression, and cecal microbiome in vivo (Gallus gallus), a clinically validated model. For this, Gallus gallus eggs were divided into six treatment groups (non-injected, 18 Ω H₂O, 1% CFWE, 2% CFWE, 5% CFWE, and 10% CFWE) with n~10 for each group. On day 17 of incubation, 1 mL of the extracts/control were administered in the amnion of the eggs. The amniotic fluid along with the administered extracts are orally consumed by the developing embryo over the course of the next few days. On day 21, the hatchlings were euthanized, the blood, duodenum, and cecum were harvested for assessment. The results showed a significant dose-dependent decrease in hemoglobin concentration, villus surface area, goblet cell number, and diameter. Furthermore, we observed a significant increase in Paneth cell number and Mucin 2 (MUC2) gene expression proportional to the increase in CFWE concentration. Additionally, the cecum microbiome analysis revealed C. sativus flower water extract altered the bacterial populations. There was a significant dose-dependent reduction in Lactobacillus and Clostridium sp., suggesting an antibacterial effect of the extract on the gut in the given model. These results suggest that the dietary consumption of C. sativus flower may have negative effects on BBM functionality, morphology, mineral absorption, microbial populations, and iron status.

Development of a 3D-Printed High Temperature Resin Cecal Fistula Implant for Long-Term and Minimally Invasive Access to the Gut Microbiome

Microbiota dysbiosis has been associated with chronic diseases ranging from gastrointestinal inflammatory and metabolic conditions to neurological changes affecting the gut-brain neural axis, mental health, and general well-being. However, current animal studies using oral gavage and gnotobiotic animals do not allow for non-invasive long-term access to gut microbiome. The purpose of the present study was to evaluate the feasibility of 3D-printed fistula implants through the body wall and into the cecum of rats to obtain long-term access to gut microbiome. Cecal fistulas were designed and 3D-printed using a high temperature resin (Formlabs; acrylic and methacrylic mixture). Nine male Sprague-Dawley rats underwent the fistula implantation. Food intake, body weight, and body fat were measured to determine the impact of fistula manipulation. Gut microbiome, vagal afferents in the hindbrain, and microglia activation were analyzed to determine if fistula implantation disrupted the gut-brain neural axis. We found that the procedure induced a transient decrease in microbial diversity in the gut that resolved within a few weeks. Fistula implantation had no impact on food intake, body weight, fat mass, or microglia activation. Our study shows that 3D-printed cecal fistula implantation is an effective procedure that allows long-term and minimally invasive access to gut microbiome.

The Nutritional Supplement L-Alpha Glycerylphosphorylcholine Promotes Atherosclerosis

L-alpha glycerylphosphorylcholine (GPC), a nutritional supplement, has been demonstrated to improve neurological function. However, a new study suggests that GPC supplementation increases incident stroke risk thus its potential adverse effects warrant further investigation. Here we show that GPC promotes atherosclerosis in hyperlipidemic Apoe-/- mice. GPC can be metabolized to trimethylamine N-oxide, a pro-atherogenic agent, suggesting a potential molecular mechanism underlying the observed atherosclerosis progression. GPC supplementation shifted the gut microbial community structure, characterized by increased abundance of Parabacteroides, Ruminococcus, and Bacteroides and decreased abundance of Akkermansia, Lactobacillus, and Roseburia, as determined by 16S rRNA gene sequencing. These data are consistent with a reduction in fecal and cecal short chain fatty acids in GPC-fed mice. Additionally, we found that GPC supplementation led to an increased relative abundance of choline trimethylamine lyase (cutC)-encoding bacteria via qPCR. Interrogation of host inflammatory signaling showed that GPC supplementation increased expression of the proinflammatory effectors CXCL13 and TIMP-1 and activated NF-κB and MAPK signaling pathways in human coronary artery endothelial cells. Finally, targeted and untargeted metabolomic analysis of murine plasma revealed additional metabolites associated with GPC supplementation and atherosclerosis. In summary, our results show GPC promotes atherosclerosis through multiple mechanisms and that caution should be applied when using GPC as a nutritional supplement.

Streptozotocin-induced hyperglycemia alters the cecal metabolome and exacerbates antibiotic-induced dysbiosis

It is well established in the microbiome field that antibiotic (ATB) use and metabolic disease both impact the structure and function of the gut microbiome. But how host and microbial metabolism interacts with ATB susceptibility to affect the resulting dysbiosis remains poorly understood. In a streptozotocin-induced model of hyperglycemia (HG), we use a combined metagenomic, metatranscriptomic, and metabolomic approach to profile changes in microbiome taxonomic composition, transcriptional activity, and metabolite abundance both pre- and post-ATB challenge. We find that HG impacts both microbiome structure and metabolism, ultimately increasing susceptibility to amoxicillin. HG exacerbates drug-induced dysbiosis and increases both phosphotransferase system activity and energy catabolism compared to controls. Finally, HG and ATB co-treatment increases pathogen susceptibility and reduces survival in a Salmonella enterica infection model. Our data demonstrate that induced HG is sufficient to modify the cecal metabolite pool, worsen the severity of ATB dysbiosis, and decrease colonization resistance.

Lactobacillus acidophilus Supplementation Exerts a Synergistic Effect on Tacrolimus Efficacy by Modulating Th17/Treg Balance in Lupus-Prone Mice via the SIGNR3 Pathway

Objective

Tacrolimus (Tac) is an immunosuppressant used in the treatment of systemic lupus erythematosus (SLE); however, it induces T cell subset imbalances by reducing regulatory T (Treg) cells. Lactobacillus acidophilus (LA) is reported to have therapeutic efficacy in immune-mediated diseases via T cell regulation.

Methods

This study investigated whether a combination therapy of LA and Tac improves the therapeutic efficacy of Tac by modulating T cell subset populations in an animal model of SLE. Eight-week-old MRL/lpr mice were orally administered with 5 mg/kg of Tac and/or 50 mg/kg of LA daily for 8 weeks. Cecal microbiota compositions, serum autoantibodies levels, the degree of proteinuria, histological changes in the kidney, and populations of various T cell subsets in the spleen were analyzed.

Results

Mice presented with significant gut dysbiosis, which were subsequently recovered by the combination treatment of Tac and LA. Double negative T cells in the peripheral blood and spleens of MRL/lpr mice were significantly decreased by the combination therapy. The combination treatment reduced serum levels of anti-dsDNA antibodies and Immunoglobulin G2a, and renal pathology scores were also markedly alleviated. The combination therapy induced Treg cells and decreased T helper 17 (Th17) cells both in vitro and in vivo. In vitro treatment with LA induced the production of indoleamine-2,3-dioxygenase, programmed death-ligand 1, and interleukin-10 via the specific intracellular adhesion molecule-3 grabbing non-integrin homolog-related 3 receptor signals.

Conclusion

The present findings indicate that LA augments the therapeutic effect of Tac and modulates Th17/Treg balance in a murine model of SLE.

Compositional Changes of the High-Fat Diet-Induced Gut Microbiota upon Consumption of Common Pulses

The gut microbiome is involved in the host's metabolism, development, and immunity, which translates to measurable impacts on disease risk and overall health. Emerging evidence supports pulses, i.e., grain legumes, as underutilized nutrient-dense, culinarily versatile, and sustainable staple foods that promote health benefits through modulating the gut microbiota. Herein, the effects of pulse consumption on microbial composition in the cecal content of mice were assessed. Male mice were fed an obesogenic diet formulation with or without 35% of the protein component comprised by each of four commonly consumed pulses-lentil (Lens culinaris L.), chickpea (Cicer arietinum L.), common bean (Phaseolus vulgaris L.), or dry pea (Pisum sativum L.). Mice consuming pulses had distinct microbial communities from animals on the pulse-free diet, as evidenced by β-diversity ordinations. At the phylum level, animals consuming pulses showed an increase in Bacteroidetes and decreases in Proteobacteria and Firmicutes. Furthermore, α-diversity was significantly higher in pulse-fed animals. An ecosystem of the common bacteria that were enhanced, suppressed, or unaffected by most of the pulses was identified. These compositional changes are accompanied by shifts in predicted metagenome functions and are concurrent with previously reported anti-obesogenic physiologic outcomes, suggestive of microbiota-associated benefits of pulse consumption.

Cinnamic acid suppresses bone loss via induction of osteoblast differentiation with alteration of gut microbiota

Osteoporosis, a disease characterized by low bone density that poses a high risk of bone fractures, is associated with aging, diet, and menopause. Despite the various known therapeutic methods for osteoporosis treatment, the development of a new therapeutic agent without side effects in long-term use is required. Cinnamic acid (CA) is a phytochemical found in cinnamon. In this study, we evaluated the effect of CA on osteoporosis and demonstrated its mechanism in MC3T3E1 preosteoblasts and ovariectomized mice. CA treatment induced osteoblast differentiation with elevation of osteogenic markers both in vitro and in vivo. CA treatment ameliorated bone loss resulting in better bone indices, increased gut microbial diversity, and recovered changes in the gut microbial composition induced by ovariectomy. These changes were accompanied by an increase in BMP/TGFβ/Smad signaling. Therefore, CA has the potential to suppress the progress of bone loss via the enhancement of bone density through the regulation of gut microbiota.

Evaluating the effects of a dietary synbiotic or synbiotic plus enhanced organic acid on broiler performance and cecal and carcass Salmonella load

Several feed additives such as synbiotics and organic acids may be viable options for controlling Salmonella in poultry. This experiment was conducted to study the effects of synbiotic product or synbiotic plus enhanced organic acid program on broiler performance, intestinal histomorphology, and cecal and carcass Salmonella load. A total of 648 day-of-hatch Cobb 700 male broiler chicks were randomly allocated to one of 4 dietary treatments: basal control diet (CON), CON diet supplemented with a synbiotic (PoultryStar; 500 g/MT; PS), CON diet supplemented with PS in the starter phase and enhanced organic acid (Biotronic PX Top3 US; 500g/MT; BPX) in the grower and finisher phase (PS1+BPX2), and the CON diet supplemented with PS in the starter and grower phase and BPX in the finisher phase (PS2+BPX1). No differences in overall BW or BWG (P > 0.05) were observed among PS, PS1+BPX2, and PS2+BPX1; however, BW was consistently greater (P < 0.05) in PS, PS1+BPX2, and PS2+BPX1 compared with CON on d 14 28, 35, and 42. On d 1 to 14 and d 1 to 28, PS and PS2+BPX1 improved FCR compared to CON (P < 0.05); PS1+BPX2 had intermediate results. No differences (P > 0.05) in overall FI were observed among dietary treatments, although PS1+BP2 and PS2+BPX1 increased FI numerically compared to CON and PS. Both PS1+BPX2 and PS2+BPX1 had reduced carcass Salmonella load by 1.6 and 1.4 log units, respectively, compared with CON (P < 0.05); PS had intermediate results. Birds fed PS1+BPX2 and PS2+BPX1 reduced the percentage of postchilled carcasses that tested positive for Salmonella by 72% and 57%, respectively, compared to CON, while PS had intermediate results with a 43% reduction. This experiment demonstrated that dietary supplementation with synbiotic or synbiotic plus organic acid can be used as a potential tool to improve growth performance and reduce carcass Salmonella in broilers.

Dietary inulin supplementation modulates the composition and activities of carbohydrate-metabolizing organisms in the cecal microbiota of broiler chickens

Inulin is a highly effective prebiotic and an attractive alternative to antibiotic growth promoters for increasing production and maintaining health in chickens. However, how inulin elicits its effects on members of the intestinal microbiota is unknown, even though their importance for energy metabolism and the health of chickens is well documented. A combination of 16S rRNA Illumina sequencing and transcriptomic analysis was used to investigate the effects of supplementing a corn-based basal diet with 1, 2, or 4% inulin or 400 ppm bacitracin on the composition, diversity and activities of carbohydrate-metabolizing organisms (CMOs) in the cecal microbiota of broiler chickens. We found that members of Bacteroides were the most abundant non-starch degrading CMOs, contributing 43.6–52.1% of total glycoside hydrolase genes and 34.6–47.1% activity to the meta-transcriptomes of chickens in the different dietary groups, although members of Parabacteroides, Prevotella, Alistipes, Clostridium, Barnesiella, Blastocystis, Faecalibacterium and others were also actively involved. Inulin and bacitracin inclusion in the basal diet did not change significantly the composition or diversity of these CMOs. Inulin supplementation at three levels promoted the activities of Bacteroides, Prevotella and Bifidobacterium, and 2% level appears to be the most optimal dosage for bifidobacterial activity.

Onion leaf and synthetic additives in broiler diet: impact on splenic cytokines, serum immunoglobulins, cecal bacterial population, and muscle antioxidant status

BACKGROUND

The disadvantages associated with the use of synthetic additives in animal production could threaten human and animal health, and the safety of animal-derived foods. This study assessed the growth performance, blood chemistry, immune indices, selected caeca bacterial population, muscle antioxidant enzyme activities, and meat quality in broiler chickens fed diet supplemented with antibiotic (70% oxytetracycline +30% neomycin), tert-butylhydroxytoluene or onion leaf powder (OLP). One day old Ross 308 chicks (n = 240) were assigned randomly to either D-1, control diet (CD) without additives; D-2, CD + 0.3 g kg^-1 antibiotic +0.15 g kg^-1 tert-butylhydroxytoluene; D-3, CD + 2.5 g kg^-1 OLP; or D-4, CD + 5 g kg^-1 OLP for 42 days.

RESULTS

The D-2 and D-4 diets improved (P < 0.05) bodyweight gain and feed efficiency in broilers. Platelet and cecal Lactobacillus spp. counts were higher (P < 0.05) whereas muscle cholesterol was lower (P < 0.05) in the OLP-supplemented birds. Supplemented birds had higher (P < 0.01) splenic interleukin-10 and lower (P < 0.01) splenic tumor necrosis factor-α, immunoglobulin A, cecal E. coli and C. perfringens counts compared with the D-1 birds. The D-4 birds had the least (P < 0.05) splenic interleukin-1β. Dietary supplements increased (P < 0.05) catalase, glutathione peroxidase, and total antioxidant capacity, and lowered (P < 0.05) drip loss, malondialdehyde and carbonyl content in breast meat.

CONCLUSION

Dietary supplementation of 5 g kg^-1 OLP exerted antimicrobial, immunomodulatory, and antioxidant effects that were comparable to those of antibiotics and tert-butylhydroxytoluene in broiler chickens. © 2021 Society of Chemical Industry.

The metabolic footprint of Clostridia and Erysipelotrichia reveals their role in depleting sugar alcohols in the cecum

BACKGROUND

The catabolic activity of the microbiota contributes to health by aiding in nutrition, immune education, and niche protection against pathogens. However, the nutrients consumed by common taxa within the gut microbiota remain incompletely understood.

METHODS

Here we combined microbiota profiling with an un-targeted metabolomics approach to determine whether depletion of small metabolites in the cecum of mice correlated with the presence of specific bacterial taxa. Causality was investigated by engrafting germ-free or antibiotic-treated mice with complex or defined microbial communities.

RESULTS

We noted that a depletion of Clostridia and Erysipelotrichia from the gut microbiota triggered by antibiotic treatment was associated with an increase in the cecal concentration of sugar acids and sugar alcohols (polyols). Notably, when we inoculated germ-free mice with a defined microbial community of 14 Clostridia and 3 Erysipelotrichia isolates, we observed the inverse, with a marked decrease in the concentrations of sugar acids and polyols in cecal contents. The carbohydrate footprint produced by the defined microbial community was similar to that observed in gnotobiotic mice receiving a cecal microbiota transplant from conventional mice. Supplementation with sorbitol, a polyol used as artificial sweetener, increased cecal sorbitol concentrations in antibiotic-treated mice, which was abrogated after inoculation with a Clostridia isolate able to grow on sorbitol in vitro.

CONCLUSIONS

We conclude that consumption of sugar alcohols by Clostridia and Erysipelotrichia species depletes these metabolites from the intestinal lumen during homeostasis. Video abstract.

Maternal cecal microbiota transfer rescues early-life antibiotic-induced enhancement of type 1 diabetes in mice

Early-life antibiotic exposure perturbs the intestinal microbiota and accelerates type 1 diabetes (T1D) development in the NOD mouse model. Here, we found that maternal cecal microbiota transfer (CMT) to NOD mice after early-life antibiotic perturbation largely rescued the induced T1D enhancement. Restoration of the intestinal microbiome was significant and persistent, remediating the antibiotic-depleted diversity, relative abundance of particular taxa, and metabolic pathways. CMT also protected against perturbed metabolites and normalized innate and adaptive immune effectors. CMT restored major patterns of ileal microRNA and histone regulation of gene expression. Further experiments suggest a gut-microbiota-regulated T1D protection mechanism centered on Reg3γ, in an innate intestinal immune network involving CD44, TLR2, and Reg3γ. This regulation affects downstream immunological tone, which may lead to protection against tissue-specific T1D injury.