Short-term high-intensity interval training exercise does not affect gut bacterial community diversity or composition of lean and overweight men.

NEW FINDINGS: What is the central question of this study? Does short-term high-intensity interval training alter the composition of the microbiome and is this associated with exercise-induced improvements in cardiorespiratory fitness and insulin sensitivity? What is the main finding and its importance? Although high-intensity interval training increased insulin sensitivity and cardiovascular fitness, it did not alter the composition of the microbiome. This suggests that changes in the composition of the microbiome that occur with prolonged exercise training might be in response to changes in metabolic health rather than driving exercise training-induced adaptations. ABSTRACT: Regular exercise reduces the risk of metabolic diseases, and the composition of the gut microbiome has been associated with metabolic function. We investigated whether short-term high-intensity interval training (HIIT) altered the diversity and composition of the bacterial community and whether there were associations with markers of insulin sensitivity or aerobic fitness. Cardiorespiratory fitness ( V̇O2peak ) and body composition (dual energy X-ray absorptiometry scan) were assessed and faecal and fasted blood samples collected from 14 lean (fat mass 21 ± 2%, aged 29 ± 2 years) and 15 overweight (fat mass 33 ± 2%, aged 31 ± 2 years) men before and after 3 weeks of HIIT training (8-12 × 60 s cycle ergometer bouts at V̇O2peak power output interspersed by 75 s rest, three times per week). Gut microbiome composition was analysed by 16S rRNA gene amplicon sequencing. The HIIT significantly increased the aerobic fitness of both groups (P < 0.001) and improved markers of insulin sensitivity (lowered fasted insulin and HOMA-IR; P < 0.001) in the overweight group. Despite differences in the abundance of several bacterial taxa being evident between the lean and overweight group, HIIT did not affect the overall bacterial diversity or community structure (α-diversity or ß-diversity). No associations were found between the top 50 most abundant bacterial genera and cardiorespiratory fitness markers; however, significant associations (P < 0.05) were observed between the abundance of the bacterial species Coprococcus_3, Blautia, Lachnospiraceae_ge and Dorea and insulin sensitivity markers in the overweight group. Our results suggest that short-term HIIT does not greatly impact the overall composition of the gut microbiome, but that certain microbiome genera are associated with insulin sensitivity markers that were improved by HIIT in overweight participants.

In Vitro Ileal Fermentation is Affected More by the Fiber Source Fermented than the Ileal Microbial Composition in Growing Pigs.

Background: The fermentation of undigested material in the ileum is quantitatively important. However, the respective contributions of the microbial composition and the substrate to ileal fermentation are unclear. Objective: This aim was to investigate the contribution of microbial composition and fiber source to in vitro ileal fermentation outcomes. Methods: Thirteen ileal cannulated female pigs (Landrace/Large White; 9-wk-old; 30.5 kg body weight) were given diets containing black beans, wheat bread, chickpeas, peanuts, pigeon peas, sorghum, or wheat bran as the sole protein source for 7 d (100 g protein/kg dry matter diet). On day 7, ileal digesta were collected and stored at -80°C for microbial analysis and in vitro fermentation. For each diet, a pooled ileal inoculum was prepared to ferment different fiber sources (cellulose, pectin, arabinogalactan, inulin, fructooligosaccharides, and resistant starch) for 2 h at 37°C. Organic matter fermentability and organic acid production were determined following in vitro fermentation. Data were analyzed using a 2-way ANOVA (inoculum × fiber). Results: Forty-five percent of the identified genera in the digesta differed across diets. For instance, the number of Lactococcus was 115-fold greater (P ≤ 0.05) in the digesta of pigs fed the pigeon pea diet than for pigs fed the wheat bran diet. For both in vitro organic matter fermentability and organic acid production, there were significant (P ≤ 0.05) interactions between the inoculum and the fiber source. For instance, pectin and resistant starch resulted in 1.6- to 31-fold more (P ≤ 0.05) lactic acid production when fermented by the pigeon pea inoculum than other inocula. For specific fiber sources, statistically significant correlations were found between the number of bacteria from certain members of the ileal microbial community and fermentation outcomes. Conclusions: Both the fiber source fermented and the ileal microbial composition of the growing pig affected in vitro fermentation; however, the effect of the fiber source was predominant.Curr Dev Nutr 2023;x:xx.

Biotransformation of Rutin in In Vitro Porcine Ileal and Colonic Fermentation Models.

Quercetin, a polyphenol antioxidant, is widely distributed in food in the form of glycoside rutin, which is not readily absorbed in the gastrointestinal tract. The microbiota of the colon is known to biotransform rutin, generating quercetin aglycones that can be absorbed. We investigated the role of the ileal and colonic microbiota in rutin biotransformation using established in vitro fermentation models. Overall, a higher rate of rutin biotransformation was observed during colonic fermentation compared with ileal fermentation. The colonic microbiome showed higher potential for rutin conversion to quercetin through an increased abundance of α-rhamnosidase- and ß-glucosidase-encoding genes compared to the ileal microbiome. Nonetheless, rutin metabolism occurred rapidly during ileal fermentation (∼20% rutin disappearance after 1 h). The appearance of quercetin varied depending on the ileal inoculum and correlated with an increased abundance of Firmicutes, suggesting that quercetin absorption could be improved via modulation of the ileal microbiota.

The Gut Microbiome Is Altered in Postmenopausal Women With Osteoporosis and Osteopenia.

Osteoporosis and its precursor osteopenia are common metabolic bone diseases in postmenopausal women. A growing body of evidence suggests that the gut microbiota is involved in the regulation of bone metabolism; however, there are few studies examining how gut microbiomes in osteoporosis and osteopenia may differ from those in healthy individuals. The aim of this study was to characterize the diversity, composition, and functional gene potential of the gut microbiota of healthy, osteopenic, and osteoporotic women. Body composition, bone density, and fecal metagenomes were analyzed in 86 postmenopausal women. The women were classified as healthy, osteopenic, or osteoporotic based on T-scores. The taxonomic and functional gene compositions of the microbiome were analyzed using shotgun metagenomic sequencing. Both osteoporotic and osteopenic taxonomic compositions were found to be significantly different from healthy participants. Linear discriminant-analysis effect-size analyses identified that healthy participants had more unclassified Clostridia and methanogenic archaea (Methanobacteriaceae) than in both osteoporotic and osteopenic participants. Bacteroides was found to be more abundant in osteoporosis and osteopenia groups. Some KEGG pathways, including carbohydrate metabolism, biosynthesis of secondary metabolites, and cyanoamino acid metabolism, were found to be more abundant in both osteoporosis and osteopenia. These results show that osteoporosis and osteopenia alter the gut microbiome of postmenopausal women and identify potential microbial taxonomic and functional pathways that may be involved in this disease. © 2020 The Authors. JBMR Plus published by Wiley Periodicals LLC. on behalf of American Society for Bone and Mineral Research.

The Effects of Unfermented and Fermented Cow and Sheep Milk on the Gut Microbiota.

A variety of fermented foods have been linked to improved human health, but their impacts on the gut microbiome have not been well characterized. Dairy products are one of the most popular fermented foods and are commonly consumed worldwide. One area we currently lack data on is how the process of fermentation changes the gut microbiota upon digestion. What is even less well characterized are the possible differences between cow and other mammals' milks. Our aim was to compare the impact of unfermented skim milk and fermented skim milk products (milk/yogurt) originating from two species (cow/sheep) on the gut microbiome using a rat model. Male Sprague-Dawley rats were fed a dairy-free diet supplemented with one of four treatment dairy drinks (cow milk, cow yogurt, sheep milk, sheep yogurt) for 2 weeks. The viable starter culture bacteria in the yogurts were depleted in this study to reduce their potential influence on gut bacterial communities. At the end of the study, cecal samples were collected and the bacterial community profiles determined via 16S rRNA high-throughput sequencing. Fermentation status drove the composition of the bacterial communities to a greater extent than their animal origin. While overall community alpha diversity did not change among treatment groups, the abundance of a number of taxa differed. The cow milk supplemented treatment group was distinct, with a higher intragroup variability and a distinctive taxonomic composition. Collinsella aerofaciens was of particularly high abundance (9%) for this group. Taxa such as Firmicutes and Lactobacillus were found in higher abundance in communities of rats fed with milk, while Proteobacteria, Bacteroidetes, and Parabacteroides were higher in yogurt fed rats. Collinsella was also found to be of higher abundance in both milk (vs. yogurt) and cows (vs. sheep). This research provides new insight into the effects of unfermented vs. fermented milk (yogurt) and animal origin on gut microbial composition in a healthy host. A number of differences in taxonomic abundance between treatment groups were observed. Most were associated with the effects of fermentation, but others the origin species, or in the case of cow milk, unique to the treatment group. Future studies focusing on understanding microbial metabolism and interactions, should help unravel what drives these differences.

Antibiotic Treatment Drives the Diversification of the Human Gut Resistome.

Despite the documented antibiotic-induced disruption of the gut microbiota, the impact of antibiotic intake on strain-level dynamics, evolution of resistance genes, and factors influencing resistance dissemination potential remains poorly understood. To address this gap we analyzed public metagenomic datasets from 24 antibiotic treated subjects and controls, combined with an in-depth prospective functional study with two subjects investigating the bacterial community dynamics based on cultivation-dependent and independent methods. We observed that short-term antibiotic treatment shifted and diversified the resistome composition, increased the average copy number of antibiotic resistance genes, and altered the dominant strain genotypes in an individual-specific manner. More than 30% of the resistance genes underwent strong differentiation at the single nucleotide level during antibiotic treatment. We found that the increased potential for horizontal gene transfer, due to antibiotic administration, was ∼3-fold stronger in the differentiated resistance genes than the non-differentiated ones. This study highlights how antibiotic treatment has individualized impacts on the resistome and strain level composition, and drives the adaptive evolution of the gut microbiota.

Characterizing the diversity of active bacteria in soil by comprehensive stable isotope probing of DNA and RNA with H218 O.

Current limitations in culture-based methods have lead to a reliance on culture-independent approaches, based principally on the comparative analysis of primary semantides such as ribosomal gene sequences. DNA can be remarkably stable in some environments, so its presence does not indicate live bacteria, but extracted ribosomal RNA (rRNA) has previously been viewed as an indicator of active cells. Stable isotope probing (SIP) involves the incorporation of heavy isotopes into newly synthesized nucleic acids, and can be used to separate newly synthesized from existing DNA or rRNA. H218 O is currently the only potential universal bacterial substrate suitable for SIP of entire bacterial communities. The aim of our work was to compare soil bacterial community composition as revealed by total versus SIP-labeled DNA and rRNA. Soil was supplemented with H218 O and after 38 days the DNA and RNA were co-extracted. Heavy nucleic acids were separated out by CsCl and CsTFA density centrifugation. The 16S rRNA gene pools were characterized by DGGE and pyrosequencing, and the sequence results analyzed using mothur. The majority of DNA (~60%) and RNA (~75%) from the microcosms incubated with H218 O were labeled by the isotope. The analysis indicated that total and active members of the same type of nucleic acid represented similar community structures, which suggested that most dominant OTUs in the total nucleic acid extracts contained active members. It also supported that H218 O was an effective universal label for SIP for both DNA and RNA. DNA and RNA-derived diversity was dissimilar. RNA from this soil more comprehensively recovered bacterial richness than DNA because the most abundant OTUs were less numerous in RNA than DNA-derived community data, and dominant OTU pools didn't mask rare OTUs as much in RNA.

Cultivation-based multiplex phenotyping of human gut microbiota allows targeted recovery of previously uncultured bacteria.

The human gut microbiota is linked to a variety of human health issues and implicated in antibiotic resistance gene dissemination. Most of these associations rely on culture-independent methods, since it is commonly believed that gut microbiota cannot be easily or sufficiently cultured. Here, we show that carefully designed conditions enable cultivation of a representative proportion of human gut bacteria, enabling rapid multiplex phenotypic profiling. We use this approach to determine the phylogenetic distribution of antibiotic tolerance phenotypes for 16 antibiotics in the human gut microbiota. Based on the phenotypic mapping, we tailor antibiotic combinations to specifically select for previously uncultivated bacteria. Utilizing this method we cultivate and sequence the genomes of four isolates, one of which apparently belongs to the genus Oscillibacter; uncultivated Oscillibacter strains have been previously found to be anti-correlated with Crohn's disease.

GC-clamp primer batches yield 16S rRNA gene amplicon pools with variable GC clamps, affecting denaturing gradient gel electrophoresis profiles.

Fingerprinting methods such as denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene pools have become a popular tool for comparisons between microbial communities. The GC-clamp portion of primers for DGGE amplicon preparation provides a key component in resolving fragments of similar size but different sequence. We hypothesized that repeat syntheses of identical 40-base GC-clamp primers lead to different DGGE profiles. Three repeat syntheses of the same GC-clamp primer and two different GC-clamp primers directed at the V3-5 region of the 16S rRNA gene were compared. Genomic DNA of two separate soil bacterial communities and three bacterial species was amplified and resolved by DGGE. The DGGE profiles obtained with repeat-synthesized primers differed among each other as much as with alternate primers, for both soil DNA and pure single species. The GC-clamp portion of members of amplicon pools varied among each other, deviating from the design sequence, and was the likely cause for multiple bands derived from a single 16S rRNA gene sequence. We recommend procuring an oligonucleotide batch large enough to conduct an entire project. This should help to avoid any DGGE profile variations due to performance differences between repeat syntheses of GC-clamp oligonucleotide primers.