Microbial management

A distinct microbiota signature precedes the clinical diagnosis of hepatocellular carcinoma

Oral, gut, and tumor microbiota have been implicated as important regulators in the carcinogenesis and progression of gastrointestinal malignancies. However, few studies focused on the existence and association of resident microbes within different body regions. Herein, we aim to reveal the durability of the oral-gut-tumor microbiome and its diagnostic performance in hepatocellular carcinoma (HCC). Our study included two cohorts: a retrospective discovery cohort of 364 HBV-HCC patients and 160 controls with oral or fecal samples, a prospective validation cohort of 91 cases, and 124 controls for matching samples, as well as 48 HBV, and 39 HBV-cirrhosis patients for gut microbial patterns examined by 16S rRNA gene sequencing. With the random forest analysis, 10 oral and 9 gut genera that could distinguish HCC from controls in the retrospective cohort were validated among the prospective matching participants, with area under the curve (AUC) values of 0.7971 and 0.8084, respectively. When influential taxa were merged, the AUC of the consistent classifier increased to 0.9405. The performance continued to improve to 0.9811 when combined with serum levels of alpha-fetoprotein (AFP). Specifically, microbial biomarkers represented by Streptococcus displayed a constantly increasing trend during the disease transition. Furthermore, the presence of several dominant microbiota species was confirmed in hepatic tumor and non-tumor tissues with fluorescence in situ hybridization (FISH) and 5 R 16S rRNA gene sequencing. Overall, our findings based on the oral-gut-tumor microbiota provide a reliable approach for the early detection of HCC.

Bacillus pumilus and Bacillus subtilis Promote Early Maturation of Cecal Microbiota in Broiler Chickens

Mature and stable intestinal microbiota in chickens is essential for health and production. Slow development of microbiota in young chickens prolongs the precarious period before reaching mature configuration. Whether probiotics can play a role in the early maturation of intestinal microbiota is unknown. To address this, day-old chicks were assigned into six groups: NC (basal diet), PC (virginiamycin), low (BPL) and high-dose (BPH) of Bacillus pumilus, and low (BSL) and high-dose (BSH) of Bacillus subtilis. Cecal contents at days 7, 14, 28 and 42 were used to analyze the treatment and time effects on the diversity and composition of microbiota. Overall, the alpha diversity was significantly decreased in the NC group between days 7 and 14, while this decline was prevented in the Bacillus subtilis probiotic (BSL and BSH) and even reversed in the BPH group. The beta-diversity showed significant responses of microbial communities to probiotics in first two weeks of life. Analyses of the abundance of microbiota reflected that members of the family Ruminococcaceae (Ruminnococcus, Oscillospira, Faecalibacterium, Butyricicoccus, and Subdoligranulum), which were dominant in mature microbiota, were significantly higher in abundance at day 14 in the probiotic groups. Conversely, the abundance of genera within the family Lachnospiraceae (Ruminococcus, Blautia, and Coprococcus) was dominant in early dynamic microbiota but was significantly lower in the probiotic groups at day 14. The Lactobacillus and Bifidobacterium abundance was higher, while the Enterobacteriaceae abundance was lower in the probiotic groups. In summary, the probiotics efficiently helped the cecal microbiota reach mature configuration earlier in life. These results could be used for the future manipulation of microbiota from the perspective of improving poultry performance.

A synbiotic intervention modulates meta-omics signatures of gut redox potential and acidity in elective caesarean born infants

BACKGROUND

The compromised gut microbiome that results from C-section birth has been hypothesized as a risk factor for the development of non-communicable diseases (NCD). In a double-blind randomized controlled study, 153 infants born by elective C-section received an infant formula supplemented with either synbiotic, prebiotics, or unsupplemented from birth until 4 months old. Vaginally born infants were included as a reference group. Stool samples were collected from day 3 till week 22. Multi-omics were deployed to investigate the impact of mode of delivery and nutrition on the development of the infant gut microbiome, and uncover putative biological mechanisms underlying the role of a compromised microbiome as a risk factor for NCD.

RESULTS

As early as day 3, infants born vaginally presented a hypoxic and acidic gut environment characterized by an enrichment of strict anaerobes (Bifidobacteriaceae). Infants born by C-section presented the hallmark of a compromised microbiome driven by an enrichment of Enterobacteriaceae. This was associated with meta-omics signatures characteristic of a microbiome adapted to a more oxygen-rich gut environment, enriched with genes associated with reactive oxygen species metabolism and lipopolysaccharide biosynthesis, and depleted in genes involved in the metabolism of milk carbohydrates. The synbiotic formula modulated expression of microbial genes involved in (oligo)saccharide metabolism, which emulates the eco-physiological gut environment observed in vaginally born infants. The resulting hypoxic and acidic milieu prevented the establishment of a compromised microbiome.

CONCLUSIONS

This study deciphers the putative functional hallmarks of a compromised microbiome acquired during C-section birth, and the impact of nutrition that may counteract disturbed microbiome development.

TRIAL REGISTRATION

The study was registered in the Dutch Trial Register (Number: 2838 ) on 4th April 2011.

High Fat-High Fructose Diet-Induced Changes in the Gut Microbiota Associated with Dyslipidemia in Syrian Hamsters

Aim: The objective of this study was to characterize the early effects of high fructose diets (with and without high fat) on both the composition of the gut microbiota and lipid metabolism in Syrian hamsters, a reproducible preclinical model of diet-induced dyslipidemia. Methods: Eight-week-old male hamsters were fed diets consisting of high-fat/high-fructose, low-fat/high-fructose or a standard chow diet for 14 days. Stool was collected at baseline (day 0), day 7 and day 14. Fasting levels of plasma triglycerides and cholesterol were monitored on day 0, day 7 and day 14, and nonfasting levels were also assayed on day 15. Then, 16S rRNA sequencing of stool samples was used to determine gut microbial composition, and predictive metagenomics was performed to evaluate dietary-induced shifts in deduced microbial functions. Results: Both high-fructose diets resulted in divergent gut microbiota composition. A high-fat/high-fructose diet induced the largest shift in overall gut microbial composition, with dramatic shifts in the Firmicute/Bacteroidetes ratio, and changes in beta diversity after just seven days of dietary intervention. Significant associations between genus level taxa and dietary intervention were identified, including an association with Ruminococceace NK4A214 group in high-fat/high-fructose fed animals and an association with Butryimonas with the low-fat/high-fructose diet. High-fat/high-fructose feeding induced dyslipidemia with increases in plasma triglycerides and cholesterol, and hepatomegaly. Dietary-induced changes in several genus level taxa significantly correlated with lipid levels over the two-week period. Differences in microbial metabolic pathways between high-fat/high-fructose and low-fat/high-fructose diet fed hamsters were identified, and several of these pathways also correlated with lipid profiles in hamsters. Conclusions: The high-fat/high-fructose diet caused shifts in the host gut microbiota. These dietary-induced alterations in gut microbial composition were linked to changes in the production of secondary metabolites, which contributed to the development of metabolic syndrome in the host.