The bacterial communities associated with fecal types and body weight of rex rabbits

Organic Iodine Improves the Growth Performance and Gut Health of Fujian Yellow Rabbits

Organic iodine is a new trace element additive that is highly efficient in regulating cell growth, function, and metabolism. This study demonstrated that organic iodine improves the growth performance and gut health of Fujian yellow rabbits. A total of 160 healthy rabbits of similar weight were randomly divided into four groups, which were treated with organic iodine (0, 0.5, 1.0, and 1.5 mg/kg) for 60 days. Our results indicated that organic iodine improved the growth performance, including significantly increased BW, ADG, and ADFI, and decreased F/G notably. Organic iodine improved the content of T3, T4, IgM, IgA, and IgM in serum, and intestinal mucosal immunity (IL-1α, IL-2, and sIgA). Organic iodine supplementation ameliorated gut morphometry and morphology, such as higher villus height and lower crypt depth. Organic iodine increased the amount of goblet cells significantly. The 0.5 mg/kg organic iodine most increased the activities of amylase, cellulase, and trypsin in caecum. Organic iodine induced more active caecum fermentation, higher NH3-N, acetic acid, propionic acid, and butyric acid, while lowering PH. In conclusion, organic iodine improved the growth performance and gut morphometry and morphology, and increased caecum enzyme activities, active caecum fermentation, and intestinal immunity of Fujian yellow rabbits.

Novel mechanism of Clostridium butyricum alleviated coprophagy prevention-induced intestinal inflammation in rabbit

As bacteria synthesize nutrients primarily in the cecum, coprophagy is indispensable for supplying rabbits with essential nutrients. Recent research has demonstrated its pivotal role in maintaining intestinal microbiota homeostasis and immune regulation in rabbits, although the specific mechanism remains unknown. Here, we used coprophagy prevention (CP) to investigate the effects of coprophagy on the cecum homeostasis and microbiota in New Zealand white rabbits. Furthermore, whether supplementation of Clostridium butyricum (C. butyricum) may alleviate the cecum inflammation and apoptosis caused by CP was also explored. Four groups were randomly assigned: control (Con), sham-coprophagy prevention (SCP), coprophagy prevention (CP), and CP and C. butyricum addition (CPCB). Compared to Con and SCP, CP augmented cecum inflammation and apoptosis, as well as bacterial adhesion to the cecal epithelial mucosa, while decreasing the expression of tight junction proteins (ZO-1, occluding, and claudin-1). The relative abundance of short-chain fatty acids (SCFAs)-producing bacteria was significantly decreased in the CP group. Inversely, there was an increase in the Firmicutes/Bacteroidetes ratio and the relative abundance of Christensenellaceae_R-7_group. Additionally, CP increased the levels of Flagellin, IFN-γ, TNF-a, and IL-1β in cecum contents and promoted the expression of TLR5/MyD88/NF-κB pathway in cecum tissues. However, the CPCB group showed significant improvements in all parameters compared to the CP group. Dietary C. butyricum supplementation significantly increased the production of SCFAs, particularly butyric acid, triggering anti-inflammatory, tissue repairing, and barrier-protective responses. Notably, CPCB effectively mitigated CP-induced apoptosis and inflammation. In summary, CP disrupts the cecum epithelial barrier and induces inflammation in New Zealand white rabbits, but these effects can be alleviated by C. butyricum supplementation. This process appears to be largely associated with the TLR5/MyD88/NF-κB signaling pathway.

Akkermansia muciniphila: a potential candidate for ameliorating metabolic diseases

Metabolic diseases are comprehensive disease based on obesity. Numerous cumulative studies have shown a certain correlation between the fluctuating abundance of Akkermansia muciniphila and the occurrence of metabolic diseases. A. muciniphila, a potential probiotic candidate colonized in the human intestinal mucus layer, and its derivatives have various physiological functions, including treating metabolic disorders and maintaining human health. This review systematically explicates the abundance change rules of A. muciniphila in metabolic diseases. It also details the high efficacy and specific molecules mechanism of A. muciniphila and its derivatives in treating obesity, type 2 diabetes mellitus, cardiovascular disease, and non-alcoholic fatty liver disease.

Potential Effects of Akkermansia Muciniphila in Aging and Aging-Related Diseases: Current Evidence and Perspectives

Akkermansia muciniphila (A. muciniphila) is an anaerobic bacterium that widely colonizes the mucus layer of the human and animal gut. The role of this symbiotic bacterium in host metabolism, inflammation, and cancer immunotherapy has been extensively investigated over the past 20 years. Recently, a growing number of studies have revealed a link between A. muciniphila, and aging and aging-related diseases (ARDs). Research in this area is gradually shifting from correlation analysis to exploration of causal relationships. Here, we systematically reviewed the association of A. muciniphila with aging and ARDs (including vascular degeneration, neurodegenerative diseases, osteoporosis, chronic kidney disease, and type 2 diabetes). Furthermore, we summarize the potential mechanisms of action of A. muciniphila and offer perspectives for future studies.

Effect of Food Restriction on Food Grinding in Brandt's Voles

Food grinding is supposed to be influenced by multiple factors. However, how those factors affecting this behavior remain unclear. In this study, we investigated the effect of food restriction on food grinding in Brandt's voles (Lasiopodomys brandtii), as well as the potential role of the gut microbiota in this process, through a comparison of the variations between voles with different food supplies. Food restriction reduced the relative amount of ground food to a greater extent than it lowered the relative food consumption, and altered the abundance of Staphylococcus, Aerococcus, Jeotgalicoccus, and Un--s-Clostridiaceae bacterium GM1. Fecal acetate content for the 7.5 g-food supply group was lower than that for the 15 g-food supply group. Our study indicated that food restriction could effectively inhibit food grinding. Further, Un--s-Clostridiaceae bacterium GM1 abundance, Aerococcus abundance, and acetate content were strongly related to food grinding. Variations in gut microbial abundance and short-chain fatty acid content induced by food restriction likely promote the inhibition of food grinding. These results could potentially provide guidance for reducing food waste during laboratory rodent maintenance.

Effects of Concentrate Feeding Sequence on Growth Performance, Nutrient Digestibility, VFA Production, and Fecal Microbiota of Weaned Donkeys

In this study, effects on the growth performance, nutrient digestibility, volatile fatty acids (VFA) production, and fecal microbiota of weaned donkeys were observed using different concentrate feeding sequences. Fifteen healthy 6-month-old weaned male donkeys with a body weight of 117.13 ± 10.60 kg were randomly divided into three treatment groups, including group C1 (roughage-then-concentrate), group C2 (concentrate-then-roughage), and group C3 (total mixed ration, TMR). The experiment lasted 35 d. We measured nutrient digestion by the acid-insoluble ash method and analyzed the fecal microbiota of the weaned donkeys by high-throughput sequencing of 16s rRNA genes in the V3-V4 region. The results show that group C3 obtained the best growth performance, and the digestibility of crude protein (CP) and crude extract (EE) was significantly higher than that of group C1 (p < 0.05). Acetic acid, isobutyric acid, valeric acid, isovaleric acid, and caproic acid were notably different among all groups (p < 0.05). In addition, we observed that Firmicutes and Bacteroidetes were dominant in the fecal microbes of each group, and Firmicutes was significantly higher in group C3 (p < 0.05). At the genus level, the different genera were Treponema, Rikenellaceae-RC9-gut-group, Unidentified-F082, and Bacteroidales-RF16-group (p < 0.05). The prediction of fecal microbiota function by PICRUSt indicated that different feeding sequences had minimal impact on the function of the fecal microbiota, particularly on the high-abundance pathway. In summary, the concentrate feeding sequence changed the composition of the fecal microbe of weaned donkeys.

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.

Arula-7 powder improves diarrhea and intestinal epithelial tight junction function associated with its regulation of intestinal flora in calves infected with pathogenic Escherichia coli O1

BACKGROUND

The effects of Arula-7 powder (ASP) on diarrhea and intestinal barrier function associated with its regulation of intestinal microflora in calves infected with pathogenic Escherichia coli O1 (E. coli O1) were studied.

METHOD

Twenty Holstein calves were randomly divided into four treatment groups: normal control (NC), model control (MC), 0.5 mg/kg ciprofloxacin (CIP) and 2.50 g/kg ASP groups.

RESULTS

ASP inhibited the relative abundance of Proteobacteria, Selenomonadales, and Enterobacteriales, and increased the relative abundance of Lactobacillus, Faecalibacterium, and Alloprevotella. Moreover, we demonstrated for the first time that the ASP and CIP promoted weight gain, reduced the diarrhea rate (P < 0.05), and enhanced antioxidant capacity (P < 0.05) due to the increase in average daily gain (ADG), total protein (TP), and albumin (ALB). In addition, ASP and CIP increased the expression of Zunola occludens-1 (ZO-1), Occludin, and Claudin-1 in the ileum (P < 0.05), and improved immunity due to increase levels of interleukin-2 (IL-2), interleukin-4 (IL-4), interferon-γ (IFN-γ), immunoglobulin A (IgA), and immunoglobulin G (IgG) in the serum, strengthened CD4+T levels in the ileal mucosa and reducing CD8+T and CD11c+T (P < 0.05).

CONCLUSION

Hence, The intestinal microbiota environment formed by early intervention of ASP powder has a protective effect on the intestinal mucosal function of calves infected with pathogenic E. coli. Video Abstract.

Normal bacterial flora of the oral cavity in healthy pet rabbits (Oryctolagus cuniculus)

BACKGROUND

Rabbits often suffer from dental disease, including dental abscesses and periodontal/apical infections. With odontogenic infection and abscessation, a bacterial aetiology can be proven by bacterial culture and identification. Although studies exist on the bacterial flora of dental abscesses, the information available to date on the bacterial flora of the oral cavity in healthy rabbits is limited.

OBJECTIVES

This study aims to evaluate the cultivable bacterial flora in the oral cavity of healthy, young, pet rabbits and to compare this flora with the pathologic flora of odontogenic abscesses described in the literature.

METHODS

Samples were collected from the oral cavity of 33 healthy, young pet rabbits undergoing routine procedures. Oral cavity culture specimens were collected by rolling a sterile flocked paediatric swab in the mouth. Identification was first attempted by morphological assessment, Gram staining and mass spectrometry (MALDI-TOF). Colonies that could not be identified by mass spectrometry were identified by amplification and molecular sequencing of a part of the 16s rRNA gene.

RESULTS

Bacteria were recovered from 100% of oral swabs; 220 isolates of 35 different genera of bacteria were cultured. The most frequently isolated bacteria were Streptococcus sp. (19.8%), Rothia sp. (17.9%), Enterobacter sp. (7%), Staphylococcus sp. (6.6%) and Actinomyces sp. (5.7%). Four phyla are represented: Proteobacteria (38.3%), Firmicutes (30.5%), Actinobacteria (26.9%) and Bacteroidota (4.3%).

CONCLUSIONS

A wide range of commensal bacteria are present in the mouths of rabbits. Bacterial cultures taken from cases of dental abscesses often reveal bacteria. Streptococcus sp., Staphylococcus sp. and Actinomyces sp. are frequently found in cultures from dental abscesses, in contrast to Rothia and Enterobacter species. Our findings enhance the knowledge of rabbit microbial communities throughout oral cavity.

Early life microbiota transplantation from highly feed-efficient broiler improved weight gain by reshaping the gut microbiota in laying chicken

Starting phase of laying chicken life is the building stone for rearing and production stages. Since, fecal microbial transplantation (FMT) regulates the gut microbial diversity and affects the productive performance of the bird. The aim of this study is to evaluate the effect of FMT from feed-efficient broiler chicken could program the diversity of gut microbiota and growth of recipient native slow growing egg-laying chicks. For this, a total of 150 (one-day-old) Jing Hong chicks were randomly assigned into two groups, each group consisted of 5 replicates (n = 15 bird/ replicate). The control group (CON) and FMT recipient birds (FMT) fed on basal diet, the FMT group received an oral daily dose of FMT prepared from Cobb-500 chickens. The FMT performed from the 1d to 28d of age, through the experimental period, feed intake and body weight were recorded weekly. At the end of a 28-day trial, carcass traits were assessed and cecal samples were collected for microbiome assessment via 16S rRNA-based metagenomic analysis to characterize the diversity and functions of microbial communities. The data were statistically analyzed using R software. Body weight and body weight gain increased, and FCR decreased (p = 0.01) in FMT group. The relative abundance of Firmicutes and the Firmicutes/Bacteroidetes (F/B) ratio were increased due to FMT administration (p = 0.01). A higher relative abundance of Lactobacillus, Lactococcus, and Bifidobacterium were presented in the FMT group. Meanwhile, Enterococcus, Helicobacter, and Bacteroides were more abundant in the CON group (p < 0.01). Kyoto encyclopedia of genes and genomes (KEGG) pathways for microbial functions regarding amino acid metabolism, secondary metabolites biosynthesis, carbohydrate metabolism, energy metabolism, and enzyme families, cofactors, and vitamins were significantly annotated in the FMT group. Overall, FMT administration from the donor of highly feed-efficient broilers improved weight gain by reshaping a distinct gut microbiome, which may be related to the metabolism and health in the recipients laying chicks, providing new insight on the application of the FMT technique for early life programming of laying chickens.

Microbial Diversity and Community Composition of Duodenum Microbiota of High and Low Egg-Yielding Taihang Chickens Identified Using 16S rRNA Amplicon Sequencing

The duodenum is an important digestive organ for poultry and houses a variety of microbes that help chickens to enhance nutrient absorption and improve production. To evaluate the characteristic of gut microbiome, duodenum content samples from 42-week-old native Taihang chickens with high (H) and low (L) egg-yielding were collected for 16S rRNA amplicon sequencing analysis. Consequently, 1,361,341 sequences were clustered into 2055 OTUs, with percentages of affiliation of 96.50 and 57.30% at phylum and genus levels. Firmicutes, Proteobacteria, Cyanobacteria and Bacteroidetes were the dominant phylum, with a lower ratio of Firmicutes/Bacteroidetes in H group than in L group (p < 0.05). At genus level, overrepresentation of Bacteroides, Faecalibacterim, and Enterococcus and underrepresentation of Romboutsia were found in H group. No significant difference in overall diversity of microbiota was observed between two groups. LEFSe analysis revealed Enterococcus was significantly enriched in H group. Importantly, Enterococcus and Lactobacillus were negatively correlated. Functional prediction analysis showed the proportion of microbiota involved in the metabolism process was the highest and enriched in H group. Differences in microbiota composition between the two groups, which may be related to intestinal function difference, also provide promising biomarkers for improving laying hen production.

Socializing Models During Lactation Alter Colonic Mucosal Gene Expression and Fecal Microbiota of Growing Piglets

The enrichment of the social environment during lactation alleviates the stress of weaned piglets. It is significant to understand how the enriched social environment improves the weaning stress of piglets. RNA sequencing (RNA-seq) of colonic mucosa, 16S rRNA sequencing of feces, and short-chain fatty acids (SCFAs) of colonic content were used to determine the effects of social contact during lactation. In this study, thirty litter lactating piglets were divided into intermittent social contact (ISC) group that contacted with neighbors intermittently, continuous social contact (CSC) group that contacted with neighbors starting at day (D) 14 after birth, and control (CON) group in which piglets were kept in their original litter. The piglets were weaned at D35 and regrouped at D36. The colonic mucosal RNA-seq, fecal microbes, and SCFAs of colonic contents of 63-day-old piglets were analyzed. The results of RNA-seq showed that compared with the CON group, the pathways of digestion and absorption of minerals, protein, and vitamins of piglets were changed in the ISC group, whereas the pathways of retinol metabolism and nitrogen metabolism in the colonic mucosal were affected and stimulated the immune response in the CSC group. Compared with the CON group, the abundances of pernicious microorganisms (Desulfovibrio, Pseudomonas, Brevundimonas, etc.) in the CSC group and pernicious microorganisms (Desulfovibrio, Neisseria, Sutterella, etc.) and beneficial bacteria (Bifidobacterium, Megamonas, and Prevotella_9) in the ISC group were significantly higher (p < 0.05). The abundances of proinflammatory bacteria (Coriobacteriaceae_unclassified, Coprococcus_3, and Ruminococcus_2) in the CSC group were significantly increased (p < 0.05), but the abundances of SCFAs producing bacteria (Lachnospiraceae_UCG-010, Parabacteroides, Anaerotruncus, etc.) and those of anti-inflammatory bacteria (Eubacterium, Parabacteroides, Ruminiclostridium_9, and Alloprevotella) were significantly reduced (p < 0.05) in the CSC group. Compared with the CON group, the concentrations of microbial metabolites, acetate, and propionate in the colonic contents were reduced (p < 0.05) in the ISC group, whereas the concentration of acetate was reduced (p < 0.05) in the CSC group. Therefore, both ISC and CSC during lactation affected the composition of fecal microbes and changed the expression of intestinal mucosal genes related to nutrient metabolism and absorption of piglets.

Use of Bayes factors to evaluate the effects of host genetics, litter and cage on the rabbit cecal microbiota

Background

The rabbit cecum hosts and interacts with a complex microbial ecosystem that contributes to the variation of traits of economic interest. Although the influence of host genetics on microbial diversity and specific microbial taxa has been studied in several species (e.g., humans, pigs, or cattle), it has not been investigated in rabbits. Using a Bayes factor approach, the aim of this study was to dissect the effects of host genetics, litter and cage on 984 microbial traits that are representative of the rabbit microbiota.

Results

Analysis of 16S rDNA sequences of cecal microbiota from 425 rabbits resulted in the relative abundances of 29 genera, 951 operational taxonomic units (OTU), and four microbial alpha-diversity indices. Each of these microbial traits was adjusted with mixed linear and zero-inflated Poisson (ZIP) models, which all included additive genetic, litter and cage effects, and body weight at weaning and batch as systematic factors. The marginal posterior distributions of the model parameters were estimated using MCMC Bayesian procedures. The deviance information criterion (DIC) was used for model comparison regarding the statistical distribution of the data (normal or ZIP), and the Bayes factor was computed as a measure of the strength of evidence in favor of the host genetics, litter, and cage effects on microbial traits. According to DIC, all microbial traits were better adjusted with the linear model except for the OTU present in less than 10% of the animals, and for 25 of the 43 OTU with a frequency between 10 and 25%. On a global scale, the Bayes factor revealed substantial evidence in favor of the genetic control of the number of observed OTU and Shannon indices. At the taxon-specific level, significant proportions of the OTU and relative abundances of genera were influenced by additive genetic, litter, and cage effects. Several members of the genera Bacteroides and Parabacteroides were strongly influenced by the host genetics and nursing environment, whereas the family S24-7 and the genus Ruminococcus were strongly influenced by cage effects.

Conclusions

This study demonstrates that host genetics shapes the overall rabbit cecal microbial diversity and that a significant proportion of the taxa is influenced either by host genetics or environmental factors, such as litter and/or cage.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12711-022-00738-2.

Metabolic Alternations During Gestation in Dezhou Donkeys and the Link to the Gut Microbiota

The maternal intestinal microbial community changes dramatically during pregnancy and plays an important role in animal growth, metabolism, immunity and reproduction. However, our understanding of microbiota compositional dynamics during the whole pregnancy period in donkey is incomplete. This study was carried out to evaluate gut microbiota alterations as well as the correlation with serum biochemical indices, comparing pregnant donkeys to non-pregnant donkeys. A total of 18 pregnant (including EP, early-stage pregnancy; MP, middle-stage pregnancy and LP, late-stage pregnancy) and six non-pregnant (C as a control) donkey blood samples and rectum contents were collected. The results showed that pregnant donkeys had higher microbial richness than non-pregnant donkeys and that the lowest microbial diversity occurred at the EP period. Moreover, the relative abundances of the families Clostridiaceae and Streptococcaceae were significantly higher in the EP group (p < 0.05) than that in the C and MP groups, while the relative abundances of the families Lachnospiraceae and Rikenellaceae were significantly lower in the EP group (p < 0.05) than that in the C group. The predicted microbial gene functions related to the inflammatory response and apoptosis, such as Staphylococcus aureus infection, the RIG-1-like receptor signaling pathway and apoptosis, were mainly enriched in EP. Furthermore, pregnant donkeys had higher glucose levels than non-pregnant donkeys, especially at EP period. EP donkeys had lower triglyceride, total protein and albumin levels but higher malondialdehyde, interleukin 1β, interleukin 6 and tumor necrosis factor-α levels than those in the C and MP groups. Additionally, there were strong correlations between inflammatory cytokine levels and the relative abundances of genera belonging to the Clostridiaceae and Streptococcaceae families. This is the first comparative study performed in donkeys that indicates that pregnancy status (especially in the early pregnancy period) alters the gut microbiota composition, which was correlated with serum biochemical parameters. These results could provide useful information for improving the reproductive management in Dezhou donkeys.

Metagenomic Comparisons between Soft and Hard Feces of Plateau Pikas (Ochotona curzoniae)

Simple Summary

Plateau pika produces hard and soft feces with different morphology, component and microbial structure. Hard feces had more abundant Firmicutes, while soft feces had more abundant Akkermansia. The differences of microbial communities between hard and soft feces were mainly driven by core microbomes. Soft feces had a comprehensive advances in predict functional pathways compared to hard feces, these strengthened functional pathways were closely associated with metabolism of energy, vitamins, and amino acid. Our study preliminarily explored the differences in microbial structure and function between hard and soft feces, provided a foundation for future systematic explorations of the cecotrophy.

Abstract

The division of hard and soft feces is an effective digestion strategy in the order Lagomorpha. Although previous studies have reported that hard and soft feces differ in morphology and component, the discrepancy in the microbiome remains unclear. This study explored the microbiomes of hard and soft feces in plateau pikas by sequencing the V3 and V4 regions of 16S rDNA. We found that hard feces harbored higher Firmicutes, while soft feces harbored higher Akkermansia. Increased rare bacterial taxa were observed in hard feces compared with soft feces. Moreover, hard and soft feces displayed a greater difference in terms of core operational taxonomy units (OTUs) compared to the total OTUs. The soft feces showed enhancements in all predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) functions, indicating an advancing microbial metabolism compared to hard feces. The significantly upregulated pathways in soft feces were mainly enriched in metabolism of energy and carbohydrate, glycan biosynthesis, cofactors and vitamins, and amino acids—all of which are associated with increased contents of microbial proteins, vitamins, and short-chain fatty acids. Our study reports, for the first time, the differential microbiomes between hard and soft feces of pikas and provides direction for the future studies on cecotrophy.

The effect of sludge retention time (SRT) on the Nitrifier typical kinetics at ambient temperature under the low ammonia density

Sludge retention time (SRT) regulation is one of the essential management techniques for refined control of the main-sidestream treatment process under the low ammonia density. It is indispensable to understand the effect of SRTs changes on the Nitrifier kinetics to obtain the functional separation of the Nitrifier and the refined control of the nitrification process. In this study, Nitrifier was cultured with conditions of 35 ± 0.5 °C, pH 7.5 ± 0.2, DO 5.0 ± 0.5 mg-O/L, and SRTs were controlled for 40 d, 20 d, 10 d, and 5 d. The net growth rate (μ_m), decay rate (b), specific growth rate (μ), the yield of the Nitrifier (Y_A), temperature parameter (T_A), and inhibition coefficient (K_I) have been measured and extended with the SRT decreases. Instead, the half-saturation coefficient (K_S) decreased. In addition, the limited value of pH inhibition occurs (pH_UL), and the pH of keeping 5% maximum reaction rate (pH_LL) was in a relatively stable state. The trade of kinetics may be induced by the change of species structure of Nitrifier. The Nitrosomonas proportion was increased, and the Nitrospira was contrary with the SRT decreasing. It is a match for the functional separation of Nitrifier when SRTs was 20 d at ambient temperature under the low ammonia density. The kinetics of ammonia-oxidizing organisms (AOO) and nitrite-oxidizing organisms (NOO) in Nitrifier under different SRT conditions should be measured respectively to the refined control of the partial nitrification process in future study.

Rabbit microbiota across the whole body revealed by 16S rRNA gene amplicon sequencing

Background

Rabbit can produce meat, fur and leather, and serves as an important biomedical animal model. Understanding the microbial community of rabbits helps to raise rabbits healthily and better support their application as animal models.

Results

In this study, we selected 4 healthy Belgium gray rabbits to collect the microbial samples from 12 body sites, including skin, lung, uterus, mouth, stomach, duodenum, ileum, jejunum, colon, cecum, cecal appendix and rectum. The microbiota across rabbit whole body was investigated via 16S rRNA gene amplicon sequencing. After quality control, 46 samples were retained, and 3,148 qualified ASVs were obtained, representing 23 phyla and 264 genera. Based on the weighted UniFrac distances, these samples were divided into the large intestine (Lin), stomach and small intestine (SSin), uterus (Uter), and skin, mouth and lung (SML) groups. The diversity of Lin microbiota was the highest, followed by those of the SSin, Uter and SML groups. In the whole body, Firmicutes (62.37%), Proteobacteria (13.44%) and Bacteroidota (11.84%) were the most predominant phyla. The relative abundance of Firmicutes in the intestinal tract was significantly higher than that in the non-intestinal site, while Proteobacteria was significantly higher in the non-intestinal site. Among the 264 genera, 35 were the core microbiota distributed in all body sites. Sixty-one genera were specific in the SML group, while 13, 8 and 1 were specifically found in the Lin, SSin and Uter groups, respectively. The Lin group had the most difference with other groups, there were average 72 differential genera between the Lin and other groups. The functional prediction analysis showed that microbial function within each group was similar, but there was a big difference between the intestinal tracts and the non-intestinal group. Notably, the function of microorganism in uterus and mouth were the most different from those in the gastrointestinal sites; rabbit’s coprophagy of consuming soft feces possibly resulted in little differences of microbial function between stomach and large intestinal sites.

Conclusion

Our findings improve the knowledge about rabbit microbial communities throughout whole body and give insights into the relationship of microbial communities among different body sites in health rabbits.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02377-x.

Comprehensive functional core microbiome comparison in genetically obese and lean hosts under the same environment

Our study provides an exhaustive comparison of the microbiome core functionalities (captured by 3,936 microbial gene abundances) between hosts with divergent genotypes for intramuscular lipid deposition. After 10 generations of divergent selection for intramuscular fat in rabbits and 4.14 phenotypic standard deviations (SD) of selection response, we applied a combination of compositional and multivariate statistical techniques to identify 122 cecum microbial genes with differential abundances between the lines (ranging from -0.75 to +0.73 SD). This work elucidates that microbial biosynthesis lipopolysaccharides, peptidoglycans, lipoproteins, mucin components, and NADH reductases, amongst others, are influenced by the host genetic determination for lipid accretion in muscle. We also differentiated between host-genetically influenced microbial mechanisms regulating lipid deposition in body or intramuscular reservoirs, with only 28 out of 122 MGs commonly contributing to both. Importantly, the results of this study are of relevant interest for the efficient development of strategies fighting obesity.

Akkermansia muciniphila and host interaction within the intestinal tract

In the modern world, metabolic syndrome is one of the major health problems. Heredity, overeating, and a sedentary lifestyle are believed to be the main predisposing factors for its development. However, recent data indicate that gut microbiota plays a significant role in metabolic profile formation. In 2004, Derrien et al. isolated and characterized the bacterium Akkermansia muciniphila, which lives mainly in the human intestine and has the ability to utilize intestinal mucin. It proved to be a good candidate for the role of a new-generation probiotic due to its ability to improve the laboratory and physical indicators associated with metabolic syndrome and type 2 diabetes in mice and humans. In this review, we describe the basic microbiological characteristics of this bacterium, its main habitats, clinical effects after oral administration, and different ways of influencing the digestive tract. All these data allow us to understand the mechanism of its beneficial effects, which is important for its future introduction into the treatment of the metabolic syndrome.

The value of gut microbiota to predict feed efficiency and growth of rabbits under different feeding regimes

Gut microbiota plays an important role in nutrient absorption and could impact rabbit feed efficiency. This study aims at investigating such impact by evaluating the value added by microbial information for predicting individual growth and cage phenotypes related to feed efficiency. The dataset comprised individual average daily gain and cage-average daily feed intake from 425 meat rabbits, in which cecal microbiota was assessed, and their cage mates. Despite microbiota was not measured in all animals, consideration of pedigree relationships with mixed models allowed the study of cage-average traits. The inclusion of microbial information into certain mixed models increased their predictive ability up to 20% and 46% for cage-average feed efficiency and individual growth traits, respectively. These gains were associated with large microbiability estimates and with reductions in the heritability estimates. However, large microbiabililty estimates were also obtained with certain models but without any improvement in their predictive ability. A large proportion of OTUs seems to be responsible for the prediction improvement in growth and feed efficiency traits, although specific OTUs taxonomically assigned to 5 different phyla have a higher weight. Rabbit growth and feed efficiency are influenced by host cecal microbiota, thus considering microbial information in models improves the prediction of these complex phenotypes.

Diverse methanogens, bacteria and tannase genes in the feces of the endangered volcano rabbit (Romerolagus diazi)

Background

The volcano rabbit is the smallest lagomorph in Mexico, it is monotypic and endemic to the Trans-Mexican Volcanic Belt. It is classified as endangered by Mexican legislation and as critically endangered by the IUCN, in the Red List. Romerolagus diazi consumes large amounts of grasses, seedlings, shrubs, and trees. Pines and oaks contain tannins that can be toxic to the organisms which consume them. The volcano rabbit microbiota may be rich in bacteria capable of degrading fiber and phenolic compounds.

Methods

We obtained the fecal microbiome of three adults and one young rabbit collected in Coajomulco, Morelos, Mexico. Taxonomic assignments and gene annotation revealed the possible roles of different bacteria in the rabbit gut. We searched for sequences encoding tannase enzymes and enzymes associated with digestion of plant fibers such as cellulose and hemicellulose.

Results

The most representative phyla within the Bacteria domain were: Proteobacteria, Firmicutes and Actinobacteria for the young rabbit sample (S1) and adult rabbit sample (S2), which was the only sample not confirmed by sequencing to correspond to the volcano rabbit. Firmicutes, Actinobacteria and Cyanobacteria were found in adult rabbit samples S3 and S4. The most abundant phylum within the Archaea domain was Euryarchaeota. The most abundant genera of the Bacteria domain were Lachnoclostridium (Firmicutes) and Acinetobacter (Proteobacteria), while Methanosarcina predominated from the Archaea. In addition, the potential functions of metagenomic sequences were identified, which include carbohydrate and amino acid metabolism. We obtained genes encoding enzymes for plant fiber degradation such as endo 1,4 β-xylanases, arabinofuranosidases, endoglucanases and β-glucosidases. We also found 18 bacterial tannase sequences.

Behaviors of cadmium in rhizosphere soils and its interaction with microbiome communities in phytoremediation

Phytoremediation of cadmium (Cd) contaminated soils by accumulators or hyperaccumulators has received considerable attention. However, there is still limited information about its migration, dynamic characteristics, and interaction with microbial communities in rhizosphere. In this study, the behaviors of Cd in rhizosphere soils in phytoremediation were carefully studied and illustrated. We find that the migration rate of Cd in rhizosphere is higher than the absorption rate of Cd by roots of plants, and Cd in near-rhizosphere moves sluggishly, and near-rhizosphere soils forms a mass pool of Cd for absorption by plants. Additionally, in tall fescue and Indian mustard treatments, shoot biomasses, total extracted Cd and migration rate of Cd in near-rhizosphere soils were comparable. It suggests that shoot biomasses of plants significantly affect their extraction of heavy metals from rhizosphere soils. Biomasses of bacteria significantly increased after phytoremediation, and structures of microbiome communities of soils after phytoremediation reassembled significantly. Furthermore, Indian mustard, even with relative lower root biomasses, could better reassembled the microbiome communities in rhizosphere than tall fescue which possesses a higher developed root system. In the end, analyses of functional microorganisms in rhizosphere soils provide new insights into biological and physiochemical roles of these populations in phytoremediation.

Microbiota Changes in Fathers Consuming a High Prebiotic Fiber Diet Have Minimal Effects on Male and Female Offspring in Rats

BACKGROUND

Consuming a diet high in prebiotic fiber has been associated with improved metabolic and gut microbial parameters intergenerationally, although studies have been limited to maternal intake with no studies examining this effect in a paternal model.

METHOD

Male Sprague Dawley rats were allocated to either (1) control or (2) oligofructose-supplemented diet for nine weeks and then mated. Offspring consumed control diet until 16 weeks of age. Bodyweight, body composition, glycemia, hepatic triglycerides, gastrointestinal hormones, and gut microbiota composition were measured in fathers and offspring.

RESULTS

Paternal energy intake was reduced, while satiety inducing peptide tyrosine tyrosine (PYY) gut hormone was increased in prebiotic versus control fathers. Increased serum PYY persisted in female prebiotic adult offspring. Hepatic triglycerides were decreased in prebiotic fathers with a similar trend (p = 0.07) seen in female offspring. Gut microbial composition showed significantly reduced alpha diversity in prebiotic fathers at 9 and 12 weeks of age (p < 0.001), as well as concurrent differences in beta diversity (p < 0.001), characterized by differences in Bifidobacteriaceae, Lactobacillaceae and Erysipelotrichaceae, and particularly Bifidobacterium animalis. Female prebiotic offspring had higher alpha diversity at 3 and 9 weeks of age (p < 0.002) and differences in beta diversity at 15 weeks of age (p = 0.04). Increases in Bacteroidetes in female offspring and Christensenellaceae in male offspring were seen at nine weeks of age.

CONCLUSIONS

Although paternal prebiotic intake before conception improves metabolic and microbiota outcomes in fathers, effects on offspring were limited with increased serum satiety hormone levels and changes to only select gut bacteria.

Individual fate and gut microbiome composition in the European wild rabbit (Oryctolagus cuniculus)

Studies connecting microbiome composition and functional performance in wildlife have received little attention and understanding their connections with wildlife physical condition are sorely needed. We studied the variation in gut microbiota (hard fecal pellets) between allopatric subspecies of the European wild rabbit in wild populations and in captured individuals studied under captivity. We evaluated the influence of environmental and host-specific factors. The microbiome of wild rabbit populations reduced its heterogeneity under controlled conditions. None of the host-specific factors tested correlated with the microbiota composition. We only observed significant intra-group dispersion for the age factor. The most diverse microbiomes were rich in Ruminococcaceae potentially holding an enriched functional profile with dominance of cellulases and xylanases, and suggesting higher efficiency in the digestion of fiber-rich food. Conversely, low diversity gut microbiomes showed dominance of Enterobacteriaceae potentially rich in amylases. We preliminary noticed geographical variations in field populations with higher dominance of Ruminococcaceae in south-western than in north-eastern Spain. Spatial differences appeared not to be subspecies driven, since they were lost in captivity, but environmentally driven, although differences in social structure and behavior may also play a role that deserve further investigations. A marginally significant relationship between the Ruminococcaceae/Enterobacteriaceae ratio and potential life expectancy was observed in captive rabbits. We hypothesize that the gut microbiome may determine the efficiency of feeding resource exploitation, and can also be a potential proxy for life expectancy, with potential applications for the management of declining wild herbivorous populations. Such hypotheses remain to be explored in the future.

Effect of host breeds on gut microbiome and serum metabolome in meat rabbits

BACKGROUND

Gut microbial compositional and functional variation can affect health and production performance of farm animals. Analysing metabolites in biological samples provides information on the basic mechanisms that affect the well-being and production traits in farm animals. However, the extent to which host breeds affect the gut microbiome and serum metabolome in meat rabbits is still unknown. In this study, the differences in phylogenetic composition and functional capacities of gut microbiota in two commercial rabbit breeds Elco and Ira were determined by 16S rRNA gene and metagenomic sequencing. The alternations in serum metabolome in the two rabbit breeds were detected using ultra-performance liquid chromatography system coupled with quadrupole time of flight mass spectrometry (UPLC-QTOFMS).

RESULTS

Sequencing results revealed that there were significant differences in the gut microbiota of the two breeds studied, suggesting that host breeds affect structure and diversity of gut microbiota. Numerous breed-associated microorganisms were identified at different taxonomic levels and most microbial taxa belonged to the families Lachnospiraceae and Ruminococcaceae. In particular, several short-chain fatty acids (SCFAs) producing species including Coprococcus comes, Ruminococcus faecis, Ruminococcus callidus, and Lachnospiraceae bacterium NK4A136 could be considered as biomarkers for improving the health and production performance in meat rabbits. Additionally, gut microbial functional capacities related to bacterial chemotaxis, ABC transporters, and metabolism of different carbohydrates, amino acids, and lipids varied greatly between rabbit breeds. Several fatty acids, amino acids, and organic acids in the serum were identified as breed-associated, where certain metabolites could be regarded as biomarkers correlated with the well-being and production traits of meat rabbits. Correlation analysis between breed-associated microbial species and serum metabolites revealed significant co-variations, indicating the existence of cross-talk among host-gut microbiome-serum metabolome.

CONCLUSIONS

Our study provides insight into how gut microbiome and serum metabolome of meat rabbits are affected by host breeds and uncovers potential biomarkers important for breed improvement of meat rabbits.

Characterization of Bacterial Microbiota Composition along the Gastrointestinal Tract in Rabbits

The microbiota is extremely important for the animal's health, but, to date, knowledge on the intestinal microbiota of the rabbit is very limited. This study aimed to describe bacterial populations that inhabit the different gastrointestinal compartments of the rabbit: stomach, duodenum, jejunum, ileum, caecum, and colon. Samples of the luminal content from all compartments of 14 healthy New White Zealand rabbits were collected at slaughter and analyzed using next generation 16S rRNA Gene Sequencing. The findings uncovered considerable differences in the taxonomic levels among the regions of the digestive tract. Firmicutes were the most abundant phylum in all of the sections (45.9%), followed by Bacteroidetes in the large intestine (38.9%) and Euryarchaeota in the foregut (25.9%). Four clusters of bacterial populations were observed along the digestive system: (i) stomach, (ii) duodenum and jejunum, (iii) ileum, and (iv) large intestine. Caecum and colon showed the highest richness and diversity in bacterial species, while the highest variability was found in the upper digestive tract. Knowledge of the physiological microbiota of healthy rabbits could be important for preserving the health and welfare of the host as well as for finding strategies to manipulate the gut microbiota in order to also promote productive performance.

Association Between Tail-Biting and Intestinal Microbiota Composition in Pigs

Tail-biting (TB) in pigs is a serious behavioral disorder. It is an important challenge in swine production as it impacts animal welfare and health and the economics and safety of the pork meat supply chain. To prevent TB, approaches including enrichment material and tail docking are proposed but none are optimal. Nutrition appears to be an important factor in TB behavior, perhaps by modulating the intestinal microbiota (IM). Our aim was to assess the association between TB behavior and IM in pigs through comparisons of IM in groups of biter, bitten and non-biter/non-bitten pigs. Each group composed of 12 pigs was formed at the beginning of the growing/finishing phase based on a target behavior analysis centered on TB behavior for the biter group and a score of damages caused to the tail for the bitten group. Blood and fecal samples were collected from each pig during a TB episode, at time 0, t0, and when the TB episode was considered finished, 4 weeks later, at time 1, t1. Serum cortisol level was determined by ELISA and used as an indicator of stress. The pig's fecal microbiota was analyzed from DNA extracted from freshly collected fecal matter using amplicon sequencing of the V4 hypervariable region of the 16S rRNA gene. Serum cortisol levels were significantly higher in either the biter or bitten pig groups compared to the negative control group (p = 0.02 and p = 0.01, respectively). The microbiota alpha-diversity was not significantly different between all groups, biter, bitten and negative control. Analyses of beta-diversity, however, revealed a significant difference between either the biter or the bitten group in comparison to the non-biter/non-bitten negative control group in terms of structure and composition of the microbiota. Lactobacillus were significantly more abundant in the negative control group compared to the two other groups (p = 0.001). No significant difference was revealed between the biter and bitten groups. Quantitative real-time PCR (qPCR) confirmed that lactobacilli were more abundant in the negative control group. Our study indicates that TB behavior is associated with the IM composition in pigs.

Breeding farm, level of feeding and presence of antibiotics in the feed influence rabbit cecal microbiota

Background

The effect of the production environment and different management practices in rabbit cecal microbiota remains poorly understood. While previous studies have proved the impact of the age or the feed composition, research in the breeding farm and other animal management aspects, such as the presence of antibiotics in the feed or the level of feeding, is still needed. Characterization of microbial diversity and composition of growing rabbits raised under different conditions could help better understand the role these practices play in cecal microbial communities and how it may result in different animal performance.

Results

Four hundred twenty-five meat rabbits raised in two different facilities, fed under two feeding regimes (ad libitum or restricted) with feed supplemented or free of antibiotics, were selected for this study. A 16S rRNA gene-based assessment through the MiSeq Illumina sequencing platform was performed on cecal samples collected from these individuals at slaughter. Different univariate and multivariate approaches were conducted to unravel the influence of the different factors on microbial alpha diversity and composition at phylum, genus and OTU taxonomic levels. The animals raised in the facility harboring the most stable environmental conditions had greater, and less variable, microbial richness and diversity. Bootstrap univariate analyses of variance and sparse partial least squares-discriminant analyses endorsed that farm conditions exerted an important influence on rabbit microbiota since the relative abundances of many taxa were found differentially represented between both facilities at all taxonomic levels characterized. Furthermore, only five OTUs were needed to achieve a perfect classification of samples according to the facility where animals were raised. The level of feeding and the presence of antibiotics did not modify the global alpha diversity but had an impact on some bacteria relative abundances, albeit in a small number of taxa compared with farm, which is consistent with the lower sample classification power according to these factors achieved using microbial information.

Conclusions

This study reveals that factors associated with the farm effect and other management factors, such as the presence of antibiotics in the diet or the feeding level, modify cecal microbial communities. It highlights the importance of offering a controlled breeding environment that reduces differences in microbial cecal composition that could be responsible for different animal performance.

Effects of Rearing Conditions and Sex on Cecal Microbiota in Ducks

The intestinal microbiome influences the health of animals. However, little is known about the impact of indoor conditions and sex on intestinal microbiome diversity and composition in ducks. The present study aimed to investigate differences in the cecal microbiome between male and female ducks reared on the floor (PY group) or in cages (LY group). We also determined the relationships between cecal microbiota composition and slaughter traits, and the expression levels of mucosal and intestinal structural genes in ducks. There was a slight difference in slaughter traits among the groups, with cecum weight being significantly lighter in the LY compared with the PY group, especially in females (p < 0.05). Analysis of the alpha diversity of the cecal microbiota between males and females in the LY and PY groups showed that LY males had significantly lower diversity and richness. Beta diversity analysis demonstrated differences in the microbiota composition in relation to rearing conditions, and a significant difference between the sexes in the PY groups. The dominant bacterial phyla in duck cecum were Bacteroidetes, Firmicutes, Proteobacteria, and Fusobacteria. The relative abundances of the most common bacteria revealed that the intestinal microbiota diversity and composition were affected by both feeding conditions and sex. Several bacterial genera were detected differentially among the groups. These genera were correlated with slaughter traits and expression levels of mucosal and cecal structural genes in ducks. In conclusion, rearing conditions, sex, and associated changes in the cecal microbiota are thus associated with gut barrier functions in ducks.

The relationship between the rumen microbiome and carcass merit in Angus steers

The objective of this study was to explore the relationships between ruminal microbial populations from Angus steers that were divergent in carcass traits related to adipose accumulation. Twenty-four feedlot-finished Angus steers (age: 538 ± 21 d; body weight following lairage: 593.9 ± 43.7 kg) were slaughtered, and ruminal contents and carcass data were collected. Ruminal microbial deoxyribonucleic acid (DNA) extraction and 16S ribosomal ribonucleic acid (rRNA) gene sequencing were performed to determine microbial relative abundances, to estimate microbial diversity, and to predict microbial metabolic pathways. A variety of correlation analyses and one-way ANOVA were performed to investigate the relationships between the rumen microbiome and carcass traits. Marbling score (P = 0.001) and longissimus lipid content (P = 0.009) were positively correlated to Chao1 Richness Index, suggesting that increased intramuscular fat was associated with increased numbers of ruminal microbial species. The phyla Tenericutes and TM7 were negatively correlated (P ≤ 0.05) to marbling score and longissimus lipid content, indicating that lower abundances of these phyla may be associated with improvements in intramuscular fat content. Greater abundance of the bacterial family S24-7 was positively correlated (P = 0.002) to marbling score. Analysis by marbling classification revealed further linkages to microbial richness (P ≤ 0.063), diversity (P = 0.044), and S24-7 (P < 0.001) populations. Computational prediction of the microbial metabolic pathways revealed no differences (P ≥ 0.05) in metabolic pathway expression in rumen microbes between steers in the high- and low-marbling classes. Several phyla, families, and genera were positively correlated (P ≤ 0.05) to both rib fat thickness and yield grade. Collectively, our results suggest that microbial composition is associated to differing performance in carcass adipose traits. Overall, most of the bacterial taxa correlated to the intramuscular and subcutaneous fat depots did not overlap, suggesting the microbial population end products likely impacted adipose accumulation largely via separate adipogenic pathways of the host animal.

Uncovering the microbiome of invasive sympatric European brown hares and European rabbits in Australia

Background

European brown hares (Lepus europaeus) and European rabbits (Oryctolagus cuniculus) are invasive pest species in Australia, with rabbits having a substantially larger environmental impact than hares. As their spatial distribution in Australia partially overlaps, we conducted a comparative microbiome study to determine how the composition of gastrointestinal microbiota varies between these species, since this may indicate species differences in diet, physiology, and other internal and external factors.

Methods

We analysed the faecal microbiome of nine wild hares and twelve wild rabbits from a sympatric periurban reserve in Canberra, Australia, using a 16S rRNA amplicon-based sequencing approach. Additionally, we compared the concordance between results from Illumina and Nanopore sequencing platforms.

Results

We identified significantly more variation in faecal microbiome composition between individual rabbits compared to hares, despite both species occupying a similar habitat. The faecal microbiome in both species was dominated by the phyla Firmicutes and Bacteroidetes, typical of many vertebrates. Many phyla, including Actinobacteria, Proteobacteria and Patescibacteria, were shared between rabbits and hares. In contrast, bacteria from phylum Verrucomicrobia were present only in rabbits, while phyla Lentisphaerae and Synergistetes were represented only in hares. We did not identify phylum Spirochaetes in Australian hares; this phylum was previously shown to be present at high relative abundance in European hare faecal samples. These differences in the composition of faecal microbiota may be indicative of less discriminate foraging behaviour in rabbits, which in turn may enable them to adapt quicker to new environments, and may reflect the severe environmental impacts that this species has in Australia.

Effects of Gut Microbiome and Short-Chain Fatty Acids (SCFAs) on Finishing Weight of Meat Rabbits

Understanding how the gut microbiome and short-chain fatty acids (SCFAs) affect finishing weight is beneficial to improve meat production in the meat rabbit industry. In this study, we identified 15 OTUs and 23 microbial species associated with finishing weight using 16S rRNA gene and metagenomic sequencing analysis, respectively. Among these, butyrate-producing bacteria of the family Ruminococcaceae were positively associated with finishing weight, whereas the microbial taxa related to intestinal damage and inflammation showed opposite effects. Furthermore, interactions of these microbial taxa were firstly found to be associated with finishing weight. Gut microbial functional capacity analysis revealed that CAZymes, such as galactosidase, xylanase, and glucosidase, could significantly affect finishing weight, given their roles in regulating nutrient digestibility. GOs related to the metabolism of several carbohydrates and amino acids also showed important effects on finishing weight. Additionally, both KOs and KEGG pathways related to the membrane transportation system and involved in aminoacyl-tRNA biosynthesis and butanoate metabolism could act as key factors in modulating finishing weight. Importantly, gut microbiome explained nearly 11% of the variation in finishing weight, and our findings revealed that a subset of metagenomic species could act as predictors of finishing weight. SCFAs levels, especially butyrate level, had critical impacts on finishing weight, and several finishing weight-associated species were potentially contributed to the shift in butyrate level. Thus, our results should give deep insights into how gut microbiome and SCFAs influence finishing weight of meat rabbits and provide essential knowledge for improving finishing weight by manipulating gut microbiome.

Digestive tract microbiota of beef cattle that differed in feed efficiency

We hypothesized cattle that differed in BW gain had different digestive tract microbiota. Two experiments were conducted. In both experiments, steers received a diet that consisted of 8.0% chopped alfalfa hay, 20% wet distillers grain with solubles, 67.75% dry-rolled corn, and 4.25% vitamin/mineral mix (including monensin) on a dry matter basis. Steers had ad libitum access to feed and water. In experiment 1, 144 steers (age = 310 ± 1.5 d; BW = 503 ± 37.2 kg) were individually fed for 105 d. Ruminal digesta samples were collected from eight steers with the greatest (1.96 ± 0.02 kg/d) and eight steers with the least ADG (1.57 ± 0.02 kg/d) that were within ±0.32 SD of the mean (10.1 ± 0.05 kg/d) dry matter. In experiment 2, 66 steers (age = 396 ± 1 d; BW = 456 ± 5 kg) were individually fed for 84 d. Rumen, duodenum, jejunum, ileum, cecum, and colon digesta samples were collected from eight steers with the greatest (2.39 ± 0.06 kg/d) and eight steers with the least ADG (1.85 ± 0.06 kg/d) that were within ±0.55 SD of the mean dry matter intake (11.9 ± 0.1 kg/d). In both studies, DNA was isolated and the V1 to V3 regions of the 16S rRNA gene were sequenced. Operational taxonomic units were classified using 0.03 dissimilarity and identified using the Greengenes 16S rRNA gene database. In experiment 1, there were no differences in the Chao1, Shannon, Simpson, and InvSimpson diversity indexes or the permutation multivariate analysis of variance (PERMANOVA; P = 0.57). The hierarchical test returned six clades as being differentially abundant between steer classifications (P < 0.05). In experiment 2, Chao1, Shannon, Simpson, and InvSimpson diversity indexes and PERMANOVA between steer classified as less or greater ADG did not differ (P > 0.05) for the rumen, duodenum, ileum, cecum, and colon. In the jejunum, there tended to be a difference in the Chao1 (P = 0.09) and Simpson diversity (P = 0.09) indexes between steer classifications, but there was no difference in the Shannon (P = 0.14) and InvSimpson (P = 0.14) diversity indexes. Classification groups for the jejunum differed (P = 0.006) in the PERMANOVA. The hierarchical dependence false discovery rate procedure returned 11 clades as being differentially abundant between steer classifications in the jejunum (P < 0.05). The majority of the OTU were in the Families Corynebacteriaceae and Coriobacteriaceae. This study suggests that intestinal differences in the microbiota of ruminants may be associated with animal performance.

Comparison Between the Gut Microbiota in Different Gastrointestinal Segments of Large-Tailed Han and Small-Tailed Han Sheep Breeds with High-Throughput Sequencing

Commensal microorganisms are essential to the normal development and function of many aspects of animal biology. However, the dynamic shift patterns of the microbiota of different gut segments in sheep and the correlation between fat type large-tailed phenotype and microbiota remain poorly unknown. This study therefore sought to assess the composition and distribution of the intestinal microbiome, and compared the difference of gut microbiota from different gastrointestinal segments within breeds and same intestinal sections between breeds. For these analyses, 16S rRNA V4 regions from 4 gut sections prepared from each of six individuals (3 from each breed) were sequenced to detect the microbiome composition in these samples. These analyses revealed the presence of 51,173 operational taxonomic units distributed across 24 phyla and 420 genera in these samples, with Firmicutes and Bacteroidetes being the most prevalent phyla of microbes present in these samples. Moreover, the bacterial composition showed distinct microbial communities in different gastrointestinal segments within breed, but showed similar and relative fixed bacterial abundance in the same intestinal segments from individuals of different breeds. We also found that only a few bacterial species (Lachnospiraceae, Akkermansia) were needed to distinguish between Small-tailed Han sheep (STH) and Large-tailed Han sheep (LTH) and their metabolic process maybe influence the fat type large-tailed phenotype formation in sheep. The functional profile analysis revealed that the environment information processing, genetic information processing, and metabolic pathways were enriched in all samples. The main functional roles of the gut microbiota were amino acid metabolism, replication and repair, carbohydrate metabolism, and membrane transport. Finally, our findings suggested that distinguished gut species between STH and LTH have relative fixed and the potential correlation is existing between the intestinal microorganisms and the large-tailed phenotype trait formation of sheep, which may offer clues for further investigation to detect the roles of intestinal microbiota in the metabolism and fat deposition in the tail of sheep.

Dynamic distribution of gut microbiota in meat rabbits at different growth stages and relationship with average daily gain (ADG)

Background

The mammalian intestinal tract harbors diverse and dynamic microbial communities that play pivotal roles in host health, metabolism, immunity, and development. Average daily gain (ADG) is an important growth trait in meat rabbit industry. The effects of gut microbiota on ADG in meat rabbits are still unknown.

Results

In this study, we investigated the dynamic distribution of gut microbiota in commercial Ira rabbits from weaning to finishing and uncover the relationship between the microbiota and average daily gain (ADG) via 16S rRNA gene sequencing. The results indicated that the richness and diversity of gut microbiota significantly increased with age. Gut microbial structure was less variable among finishing rabbits than among weaning rabbits. The relative abundances of the dominant phyla Firmicutes, Bacteroidetes, Verrucomicrobia and Cyanobacteria, and the 15 predominant genera significantly varied with age. Metagenomic prediction analysis showed that both KOs and KEGG pathways related to the metabolism of monosaccharides and vitamins were enriched in the weaning rabbits, while those related to the metabolism of amino acids and polysaccharides were more abundant in the finishing rabbits. We identified 34 OTUs, 125 KOs, and 25 KEGG pathways that were significantly associated with ADG. OTUs annotation suggested that butyrate producing bacteria belong to the family Ruminococcaceae and Bacteroidales_S24-7_group were positively associated with ADG. Conversely, Eubacterium_coprostanoligenes_group, Christensenellaceae_R-7_group, and opportunistic pathogens were negatively associated with ADG. Both KOs and KEGG pathways correlated with the metabolism of vitamins, basic amino acids, and short chain fatty acids (SCFAs) showed positive correlations with ADG, while those correlated with aromatic amino acids metabolism and immune response exhibited negative correlations with ADG. In addition, our results suggested that 10.42% of the variation in weaning weight could be explained by the gut microbiome.

Conclusions

Our findings give a glimpse into the dynamic shifts in gut microbiota of meat rabbits and provide a theoretical basis for gut microbiota modulation to improve ADG in the meat rabbit industry.

Early-life intestinal microbiome in Trachemys scripta elegans analyzed using 16S rRNA sequencing

During the early-life period, the hatchlings of red-eared slider turtles (Trachemys scripta elegans) rely on their own post-hatching internal yolk for several days before beginning to feed. The gut microbiome is critical for the adaptation of organisms to new environments, but, to date, how the microbiome taxa are assembled during early life of the turtle is unknown. In this study, the intestinal microbiome of red-eared slider hatchlings (fed on commercial particle food) was systematically analyzed at four different growth stages (0 d, 10 d, 20 d, 30 d) by a high-throughput sequencing approach. Results showed that the dominant phyla were Firmicutes (58.23%) and Proteobacteria (41.42%) at 0-day, Firmicutes (92.94%) at 10-day, Firmicutes (67.08%) and Bacteroidetes (27.17%) at 20-day, and Firmicutes (56.46%), Bacteroidetes (22.55%) and Proteobacteria (20.66%) at 30-day post-hatching. Members of the Bacteroidaceae family were absent in 0-day and 10-day turtles, but dominated in 20-day and 30-day turtles. The abundance of Clostridium also showed the highest value in 10-day turtles. The richness of the intestinal microbiomes was lower at 0-day and 30-day than that at 10-day and 20-day, while the diversity was higher at 10-day and 30-day than that at 0-day and 20-day. The results endowed the turtles with an ability to enhance their tolerance to the environment.

Influence of cecotrophy on fat metabolism mediated by caecal microorganisms in New Zealand white rabbits

Cecotrophy is a special behaviour of rabbits. Eating soft faeces can improve feed efficiency and maintain gut flora in rabbits. In our previous study, we found that fasting from soft faeces significantly reduced growth rate and total cholesterol (TC) in New Zealand white rabbits (NZW rabbits), thereby resulting in lower values for body weight and fat deposition in the soft faeces fasting group than in the control group. However, it has not been demonstrated whether cecotrophy by NZW rabbits can regulate lipid metabolism by changing the diversity of caecal microorganisms. In this study, thirty-six 28-day-old weaned NZW female rabbits were randomly divided into two groups (the soft faeces fasting group and the control group) and fed to 90 days. Rabbits in the experimental group were treated with an Elizabeth circle to prevent them from eating their soft faeces. Then, the caecal contents of three rabbits from the soft faeces fasting group and three rabbits from the control group were collected for metagenomic sequencing. We found that the abundance of Bacteroides increased, while Ruminococcus decreased, compared with the control group after fasting from soft faeces. Relative abundance was depressed for genes related to metabolic pathways such as ascorbate and aldarate metabolism, riboflavin metabolism and bile secretion. Moreover, there was a general correlation between variation in microbial diversity and fat deposition. Bacteroides affects body weight and TC by participating in the riboflavin metabolism pathway. By investigating the effect of cecotrophy on caecal microorganisms of rabbits, we identified the key microorganisms that regulate the rapid growth performance of NZW rabbits, which may provide useful reference for the future research and development of microecological preparations for NZW rabbits.

Effects of Allium hookeri on gut microbiome related to growth performance in young broiler chickens

Healthy food promotes beneficial bacteria in the gut microbiome. A few prebiotics act as food supplements to increase fermentation by beneficial bacteria, which enhance the host immune system and health. Allium hookeri is a healthy food with antioxidant and anti-inflammatory activities. A. hookeri is used as a feed supplement for broiler chickens to improve growth performance. Although the underlying mechanism is unknown, A. hookeri may alter the gut microbiome. In the current study, 16S rRNA sequencing has been carried out using samples obtained from the cecum of broiler chickens exposed to diets comprising different tissue types (leaf and root) and varying amounts (0.3% and 0.5%) of A. hookeri to investigate their impact on gut microbiome. The microbiome composition in the groups supplemented with A. hookeri leaf varied from that of the control group. Especially, exposure to 0.5% amounts of leaf resulted in differences in the abundance of genera compared with diets comprising 0.3% leaf. Exposure to a diet containing 0.5% A. hookeri leaf decreased the abundance of the following bacteria: Eubacterium nodatum, Marvinbryantia, Oscillospira, and Gelria. The modulation of gut microbiome by leaf supplement correlated with growth traits including body weight, bone strength, and infectious bursal disease antibody. The results demonstrate that A. hookeri may improve the health benefits of broiler chickens by altering the gut microbiome.

Responses of microbial community to different concentration of perchlorate in the Qingyi River

Perchlorate is a refractory and mobile contaminant that is wildly distributed in surface water, and due to its tremendous inhibitory effect on mammalian thyroid function, it has gained much attention in recent years. Numerous studies have focused on environmental detection of perchlorate, especially in water. However, less attention has been paid to the effects of perchlorate on the composition of the microbial community in rivers. Upstream of the Qingyi River, an important source of drinking water for local residents, there are two perchlorate manufacturers. In this study, we selected eight study sites from upstream to downstream of the Qingyi River, including sites located upstream and downstream of the perchlorate manufacturers. Our results indicated that perchlorate was detected in all sites except for QYR2, QYR3, and QYR10. The concentration of perchlorate in the five study sites was much higher than the reference dose proposed by the National Academy of Science, and ranged from 187 to 9647.00 μg/L. We utilized 16S rDNA high throughput sequencing to analyze changes in the composition of the microbial community, based on the Illumina 2 × 250 MiSeq platform. The results showed that, when microbial communities were exposed to high concentration of perchlorate, there was an increase in the ratio of Betaproteobacteria, Bacteroidetes, Actinobacteria, and Saccharibacteria in the microbial community along with a decrease in the ratio of Chloroflexi, Verrucomicrobia, and Gammaproteobacteria. Our study has provided a theoretical basis for the alteration of the microbial community caused by the perchlorate pollution, which maybe have a truly important impact on the quality of groundwater.

Faecal microbiota and functional capacity associated with weaning weight in meat rabbits

Weaning weight is an important economic trait in the meat rabbit industry. Evidence has linked the gut microbiota to health and production performance in rabbits. However, the effect of gut microbiota on meat rabbit weaning weight remains unclear. In this study, we performed 16S rRNA gene sequencing analysis of 135 faecal samples from commercial Ira rabbits. We detected 50 OTUs significantly associated with weaning weight. OTUs that showed positive associations with weaning weight were mostly members of the family Ruminococcaceae which are important in degrading dietary fibres and producing butyrate. On the contrary, OTUs annotated to genera Blautia, Lachnoclostridium and Butyricicoccus correlated with fat deposition were negatively associated with weaning weight. Predicted functional capacity analysis revealed that 91 KOs and 26 KEGG pathways exhibited potential correlations with weaning weight. We found that gut microbiota involved in the metabolism of amino acids, butanoate, energy and monosaccharides affected weaning weight. Additionally, cross-validation analysis indicated that 16.16% of the variation in weaning weight was explained by the gut microbiome. Our findings provide important information to improve weaning weight of meat rabbits by modulating their gut microbiome.

Comparative characterization of bacterial communities in geese consuming of different proportions of ryegrass

Geese are extremely well-adapted to utilizing plant-derived roughage in their diet, so the grass must be added to commercial diets under intensive rearing systems. However, it is unclear whether the gut microbiota will change significantly when adding different proportions of ryegrass. In this study, 240 healthy male Yangzhou geese (28 days old) with similar body weights were randomly divided into four groups and fed different proportions grass (CK, whole commercial diets; EG1, ryegrass: commercial diets = 1.5:1; EG2, ryegrass: commercial diets = 2:1; EG3, ryegrass: commercial diets = 3:1) respectively. When the geese grew to 70 days old, their intestines were collected and high-throughput sequencing technology was performed to investigate the microbial diversity in the caecum of geese with different dietary supplements. There was no obvious change in the alpha diversity of gut microbiota of geese with ryegrass intake (P > 0.05) and the composition of dominant bacterium (including Bacteroidetes and Firmicutes) was also similar. However, the ratio between Firmicutes and Bacteroidetes was remarkably reduced with ryegrass intake (P < 0.05), and the relative abundance of 30 operational taxonomic units (OTUs) significantly differed. Additionally, the content of cellulose-degrading microbiota such as Ruminiclostridium and Ruminococcaceae UCG-010 were significantly increased in geese fed with increasing amounts of grass. Finally, the functional profiles of the goose gut microbiota were explored using the PICRUSt tool. Carbohydrate metabolism and amino acid metabolism were dominant metabolic pathways. Lipid metabolism was significantly increased in EG3 compared that in the CK group (P < 0.05). Interestingly, Turicibacter and Parasutterella may have affected abdominal fat deposition as grass intake increased. Taken together, although the diversity of bacterial communities was similar in geese fed with different proportions of ryegrass, cellulose-degrading microbiota (Ruminiclostridium and Ruminococcaceae UCG-010) were abundant and the lipid metabolic pathway was enriched, which may reduce abdominal fat accumulation in high-ryegrass fed geese.

Preliminary Study on the Effect of Bacillus amyloliquefaciens TL on Cecal Bacterial Community Structure of Broiler Chickens

Probiotics can promote the health and growth performance of animals through modulation of intestinal microbiota. When used as a feed additive, they have the potential to minimize or abolish the use of antibiotics. In this study, we investigated the effect of the probiotic strain Bacillus amyloliquefaciens TL on the growth performance and cecum microflora composition in Cobb 500 broiler chickens. In total, 180 broilers were randomly divided into three groups-each group comprised 4 pens, and each pen contained 15 chickens. The three groups were fed either a control diet, or a diet supplemented with either the antibiotic chlortetracycline or B. amyloliquefaciens TL. Broilers were weighed, and cecum contents were collected on days 7, 14, 21, and 35, respectively. The broilers in both the antibiotic and probiotic groups exhibited significant weight gain compared with controls, exhibiting increases of 16.02% and 13.40%, respectively, after 35 days (P < 0.01). Similarly, the feed conversion ratio (FCR, 1-35 days) of broilers in the chlortetracycline and B. amyloliquefaciens TL groups was lower than that of the controls. HiSeq high-throughput sequencing of 16S rRNA of the cecal microbiota was performed on days 7, 14, 21, and 35, respectively. The Firmicutes/Bacteroidetes ratio was higher in the chlortetracycline and B. amyloliquefaciens TL groups than in the control group on days 14, 21, and 35, and especially on day 21. The prevalence of genera Oscillospira, Ruminococcus, Butyricicoccus, and Faecalibacterium (Firmicutes) was higher in the antibiotic and probiotic groups, while that of Bacteroides, Parabacteroides (Bacteroidetes), and Lactobacillus was higher in the control group. In this study, the changes in the microbiota of the probiotic group were similar to those in the antibiotic group. These results suggest that the probiotic strain B. amyloliquefaciens TL can modulate the cecal microbiota of broilers similar to chlortetracycline.

Transcriptome Analysis of the Effects of Fasting Caecotrophy on Hepatic Lipid Metabolism in New Zealand Rabbits

Simple Summary

Caecotrophy in small herbivores, including rabbits, is the instinctive behavior of eating soft feces. Little is known about the impact of caecotrophy on growth and metabolism. In the present study, we used an Elizabeth circle to prevent rabbits from eating soft feces and measured changes in feed intake, body weight, internal organ weight, serum biochemical indices and liver lipid droplet accumulation. Liver tissue was also used for transcriptome sequencing. Results indicated that fasting caecotrophy decreased rabbit growth and lipid synthesis in the liver.

Abstract

In order to investigate the effects of fasting caecotrophy on hepatic lipid metabolism in rabbits, 12 weaned female New Zealand white rabbits were randomly divided into (n = 6/group) a control and fasting caecotrophy group. Rabbits in the experimental group were treated with an Elizabeth circle to prevent them from eating their own soft feces for a 60-day period. Growth and blood biochemical indices, transcriptome sequencing and histology analysis of the liver were performed. Compared with the control group, final weight, weight gain, liver weight, growth rate and feed conversion ratio, all decreased in the experimental group (p < 0.05). RNA sequencing (RNA-seq) analysis revealed a total of 301.2 million raw reads (approximately 45.06 Gb of high-quality clean data) that were mapped to the rabbit genome. After a five-step filtering process, 14,964 genes were identified, including 444 differentially expressed genes (p < 0.05, foldchange ≥ 1). A number of differently expressed genes linked to lipid metabolism were further analyzed including CYP7A1, SREBP, ABCA1, GPAM, CYP3A1, RBP4 and RDH5. The KEGG (Kyoto Encyclopedia of Genes and Genomes) annotation of the differentially expressed genes indicated that main pathways affected were pentose and glucuronide interactions, starch and sucrose metabolism, retinol metabolism and PPAR signaling. Overall, the present study revealed that preventing caecotrophy reduced growth and altered lipid metabolism, both of which will help guide the development of new approaches for rabbits’ feeding and production. These data also provide a reference for studying the effects of soft feces in other small herbivores.

Variations in Gut Microbiota of Siberian Flying Squirrels Correspond to Seasonal Phenological Changes in Their Hokkaido Subarctic Forest Ecosystem

Gut microbial communities of animals are influenced by diet and seasonal weather changes. Since foraging strategies of wild animals are affected by phenological changes, gut microbial communities would differ among seasons. However, interactions of plant-animal-microbiota with seasonal changes have not been well characterized. Here, we surveyed gut microbial diversity of Siberian flying squirrels (Pteromys volans orii) from a natural forest in Hokkaido during spring and summer of 2013 and 2014. Additionally, we compared microbial diversity to temperature changes and normalized difference vegetation index (NDVI). Changes in both seasonal temperature and phenology were significantly associated with alterations in gut microbiota. There were two clusters of OTUs, below and above 20 °C that were significantly correlated with low and high temperatures, respectively. Low-temperature cluster OTUs belonged to various phyla, whereas the high-temperature cluster was only constituted by Firmicutes. In conclusion, gut microbiota of Siberian flying squirrels varied with environmental changes on an ecological scale.

Gut microbiota of newborn piglets with intrauterine growth restriction have lower diversity and different taxonomic abundances

Aim

Intrauterine growth retardation (IUGR) is a prevalent problem in mammals. The present study was conducted to unveil the alterations in intestinal microbiota in IUGR piglets.

Methods and Results

We identified the alterations of small intestinal microbiota in IUGR piglets on 7, 21 and 28 days of age using 16S rRNA sequencing. The results showed that IUGR piglets had a decreased alpha diversity of jejunum microbiota at 7 and 21 days of age; had lower abundances of Bacteroidetes and Bacteroides in the jejunum at 7, 21 and 28 days of age, Oscillibacter in the jejunum at 21 days of age, and Firmicutes in the ileum at 21 days of age; whereas they had higher abundances of Proteobacteria and Pasteurella in the ileum at 21 days of age and Escherichia–Shigella in the jejunum at 28 days of age. Correlation analysis showed that Bacteroides, Oscillibacter and Ruminococcaceae_UCG‐002 compositions were positively associated with the body weight (BW) of IUGR piglets, nevertheless Proteobacteria and Escherichia–Shigella relative abundances were negatively correlated with the BW of IUGR piglets. Gene function prediction analysis indicated that microbiota‐associated carbohydrate metabolism, lipid metabolism, glycan biosynthesis and metabolism, amino acid metabolism, and xenobiotics biodegradation and metabolism were downregulated in the IUGR piglets compared to control piglets.

Conclusions

The present study profiled the intestinal microbiota of newborn piglets with IUGR and the newborn IUGR piglets have lower diversity and different taxonomic abundances. Alterations in the abundances of Bacteroidetes, Bacteroides, Proteobacteria Escherichia–Shigella and Pasteurella may be involved in nutrient digestion and absorption, as well as the potential mechanisms connecting to the growth and development of IUGR in mammals.

Significance and Impact of the Study

The small intestinal microbiota were highly shaped in the IUGR piglets, which might further mediate the growth and development of IUGR piglets; and the gut microbiota could serve as a potential target for IUGR treatment.

Metabolites of stable fly reduce diarrhea in mice by modulating the immune system, antioxidants, and composition of gut microbiota

Escherichia coli (E. coli) O₁-induced diarrhea is associated with intestinal microbial imbalance, however, the results of using oral antibiotics still remain poor. To overcome such problem, our study investigates the role of metabolites from stable flies (MSF) in the occurrence of diarrhea. The amino acid composition and molecular weight analysis of MSF by RP-HPLC and GPC, respectively. Besides the normal control group, SPF mice in other group were inoculated with E. coli O1 received treatment as follows over a period of 7 days saline solution (E. coli control), ciprofloxacin (0.13 g/kg; positive control) and MSF (2, 4 and 8 mg/kg) dosage. Throughout the experiment, defecation and body weights were examined and recorded. On the eighth day, after administering anesthesia, blood, tissue of small intestine samples were obtained for immunological and anti-oxidant. Small intestinal tissues and cecum contents samples were used for histopathological and 16S rDNA sequencing analysis. Our showed that MSF was rich in isoleucine, and its molecular weight less than 400 Da is 60.03%. MSF (4 and 8 mg/kg) and ciprofloxacin, significantly decreased IL-6, IL-8 and TNF-α levels, whereas, increased IL-2, IL-4, IL-10, INF-γ, IgA and IgG levels in mice having diarrhea. These treatments also reversed intestinal flora imbalance as indicated by the increased in Firmicutes-to-Bacteroidetes ratio and Clostridium levels (P < 0.05) and improved 5-HT, CAT and SOD levels. MSF favored diarrhea management as compared to ciprofloxacin, suggesting that MSF can be used in the management of E. coli O₁-induced diarrhea, in normal gut microbiota and normal intestinal antioxidant function.

The combination of sport and sport-specific diet is associated with characteristics of gut microbiota: an observational study

Background

Recently, gut microbiota have been studied extensively for health promotion, disease prevention, disease treatment, and exercise performance. It is recommended that athletes avoid dietary fiber and resistant starch to promote gastric emptying and reduce gastrointestinal distress during exercise, but this diet may reduce microbial diversity and compromise the health of the athlete’s gut microbiota.

Objective

This study compared fecal microbiota characteristics using high-throughput sequencing among healthy sedentary men (as controls), bodybuilders, and distance runners, as well as the relationships between microbiota characteristics, body composition, and nutritional status.

Methods

Body composition was measured using DXA, and physical activity level was assessed using IPAQ. Dietary intake was analyzed with the computerized nutritional evaluation program. The DNA of fecal samples was extracted and it was sequenced for the analysis of gut microbial diversity through bioinformatics cloud platform.

Results

We showed that exercise type was associated with athlete diet patterns (bodybuilders: high protein, high fat, low carbohydrate, and low dietary fiber diet; distance runners: low carbohydrate and low dietary fiber diet). However, athlete type did not differ in regard to gut microbiota alpha and beta diversity. Athlete type was significantly associated with the relative abundance of gut microbiota at the genus and species level: Faecalibacterium, Sutterella, Clostridium, Haemophilus, and Eisenbergiella were the highest (p < 0.05) in bodybuilders, while Bifidobacterium and Parasutterella were the lowest (p < 0.05). At the species level, intestinal beneficial bacteria widely used as probiotics (Bifidobacterium adolescentis group, Bifidobacterium longum group, Lactobacillus sakei group) and those producing short chain fatty acids (Blautia wexlerae, Eubacterium hallii) were the lowest in bodybuilders and the highest in controls. In addition, aerobic or resistance exercise training with an unbalanced intake of macronutrients and low intake of dietary fiber led to similar diversity of gut microbiota. Specifically, daily protein intake was negatively correlated with operation taxonomic unit (r = − 0.53, p < 0.05), ACE (r = − 0.51, p < 0.05), and Shannon index (r = − 0.64, p < 0.01) in distance runners..

Conclusion

Results suggest that high-protein diets may have a negative impact on gut microbiota diversity for athletes, while athletes in resistance sports that carry out the high protein low carbohydrates diet demonstrate a decrease in short chain fatty acid-producing commensal bacteria.

The Koala (Phascolarctos cinereus) faecal microbiome differs with diet in a wild population

Background

The diet of the koala (Phascolarctos cinereus) is comprised almost exclusively of foliage from the genus Eucalyptus (family Myrtaceae). Eucalyptus produces a wide variety of potentially toxic plant secondary metabolites which have evolved as chemical defences against herbivory. The koala is classified as an obligate dietary specialist, and although dietary specialisation is rare in mammalian herbivores, it has been found elsewhere to promote a highly-conserved but low-diversity gut microbiome. The gut microbes of dietary specialists have been found sometimes to enhance tolerance of dietary PSMs, facilitating competition-free access to food. Although the koala and its gut microbes have evolved together to utilise a low nutrient, potentially toxic diet, their gut microbiome has not previously been assessed in conjunction with diet quality. Thus, linking the two may provide new insights in to the ability of the koala to extract nutrients and detoxify their potentially toxic diet.

Method

The 16S rRNA gene was used to characterise the composition and diversity of faecal bacterial communities from a wild koala population (n = 32) comprising individuals that predominately eat either one of two different food species, one the strongly preferred and relatively nutritious species Eucalyptus viminalis, the other comprising the less preferred and less digestible species Eucalyptus obliqua.

Results

Alpha diversity indices indicated consistently and significantly lower diversity and richness in koalas eating E. viminalis. Assessment of beta diversity using both weighted and unweighted UniFrac matrices indicated that diet was a strong driver of both microbial community structure, and of microbial presence/absence across the combined koala population and when assessed independently. Further, principal coordinates analysis based on both the weighted and unweighted UniFrac matrices for the combined and separated populations, also revealed a separation linked to diet. During our analysis of the OTU tables we also detected a strong association between microbial community composition and host diet. We found that the phyla Bacteroidetes and Firmicutes were co-dominant in all faecal microbiomes, with Cyanobacteria also co-dominant in some individuals; however, the E. viminalis diet produced communities dominated by the genera Parabacteroides and/or Bacteroides, whereas the E. obliqua-associated diets were dominated by unidentified genera from the family Ruminococcaceae.

Discussion

We show that diet differences, even those caused by differential consumption of the foliage of two species from the same plant genus, can profoundly affect the gut microbiome of a specialist folivorous mammal, even amongst individuals in the same population. We identify key microbiota associated with each diet type and predict functions within the microbial community based on 80 previously identified Parabacteroides and Ruminococcaceae genomes.