Extracellular fructooligosaccharide degradation in Anaerostipes hadrus for co-metabolism with non-fructooligosaccharide utilizers

Anaerostipes hadrus, a butyrate-producing bacterium capable of metabolizing 5-fluorouracil

Anaerostipes hadrus (A. hadrus) is a dominant species in the human gut microbiota and considered a beneficial bacterium for producing probiotic butyrate. However, recent studies have suggested that A. hadrus may negatively affect the host through synthesizing fatty acid and metabolizing the anticancer drug 5-fluorouracil, indicating that the impact of A. hadrus is complex and unclear. Therefore, comprehensive genomic studies on A. hadrus need to be performed. We integrated 527 high-quality public A. hadrus genomes and five distinct metagenomic cohorts. We analyzed these data using the approaches of comparative genomics, metagenomics, and protein structure prediction. We also performed validations with culture-based in vitro assays. We constructed the first large-scale pan-genome of A. hadrus (n = 527) and identified 5-fluorouracil metabolism genes as ubiquitous in A. hadrus genomes as butyrate-producing genes. Metagenomic analysis revealed the wide and stable distribution of A. hadrus in healthy individuals, patients with inflammatory bowel disease, and patients with colorectal cancer, with healthy individuals carrying more A. hadrus. The predicted high-quality protein structure indicated that A. hadrus might metabolize 5-fluorouracil by producing bacterial dihydropyrimidine dehydrogenase (encoded by the preTA operon). Through in vitro assays, we validated the short-chain fatty acid production and 5-fluorouracil metabolism abilities of A. hadrus. We observed for the first time that A. hadrus can convert 5-fluorouracil to α-fluoro-β-ureidopropionic acid, which may result from the combined action of the preTA operon and adjacent hydA (encoding bacterial dihydropyrimidinase). Our results offer novel understandings of A. hadrus, exceptionally functional features, and potential applications.

IMPORTANCE

This work provides new insights into the evolutionary relationships, functional characteristics, prevalence, and potential applications of Anaerostipes hadrus.

Association analysis of the gut microbiota in predicting outcomes for patients with acute ischemic stroke and H-type hypertension

Introduction

H-type hypertension (HHTN) is a subtype of hypertension that tends to worsen the prognosis of acute ischemic stroke (AIS). Recent studies have highlighted the vital role of gut microbiota in both hypertension and AIS, but there is little available data on the relationship between gut microbiota and the progression of AIS patients with HHTN. In this study, we investigated the microbial signature of AIS patients with HHTN and identified characteristic bacteria as biomarkers for predicting prognosis.

Methods

AIS patients with HHTN (n = 150) and without HHTN (n = 50) were enrolled. All patients received a modified Rankin Scale (mRS) assessment at 3 months after discharge. Fecal samples were collected from the participants upon admission, including 150 AIS patients with HHTN, 50 AIS patients with non-HHTN, and 90 healthy subjects with HHTN. These samples were analyzed using 16S rRNA sequencing to characterize the bacterial taxa, predict functions, and conduct correlation analysis between specific taxa and clinical features.

Results

Our results showed that the composition of the gut microbiota in HHTN patients differed significantly from that in non-HHTN patients. The abundance of the genera Bacteroides, Escherichia-Shigella, Lactobacillus, Bifidobacterium, and Prevotella in AIS patients with HHTN was significantly increased compared to AIS patients without HHTN, while the genus Streptococcus, Faecalibacterium, and Klebsiella were significantly decreased. Moreover, Bacteroides, Lactobacillus, Bifidobacterium, and Klebsiella in AIS patients with HHTN were more abundant than healthy subjects with HHTN, while Escherichia-Shigella, Blautia, and Faecalibacterium were less abundant. Moreover, the genera Butyricicoccus, Rothia, and Family_XIII_UCG-001 were negatively connected with the NIHSS score, and the genera Butyricicoccus and Rothia were observed to be negatively associated with the mRS score. The genera Butyricicoccus, Romboutsia, and Terrisporobacter were associated with a poor prognosis, whereas the increase in Butyricimonas and Odoribacter was correlated with good outcomes. Generated by eight genera and clinical indexes, the area under the curve (AUC) value of the receiver operating characteristic (ROC) curve achieved 0.739 to effectively predict the prognosis of AIS patients with HHTN.

Conclusion

These findings revealed the microbial signature of AIS patients with HHTN and further provided potential microbial biomarkers for the clinical diagnosis of AIS patients with HHTN.

Spore-forming properties and enhanced oxygen tolerance of butyrate-producing Anaerostipes spp

OBJECTIVES

Butyrate producing bacteria are promising candidates for next-generation probiotics. However, they are extremely sensitive to oxygen, which is a significant obstacle to their inclusion in food matrices in a viable form. The present study characterized the spore-forming properties and stress tolerance of human gut butyrate-producing Anaerostipes spp.

METHODS

Spore formation properties in six species of Anaerostipes spp. were studied by in vitro and in silico tests.

RESULTS

Spores were observed from the cells of three species using microscopic analyses, while the remaining three did not form spores under the tested conditions. Spore-forming properties were confirmed by an ethanol treatment. The spores of Anaerostipes caccae were tolerant to oxygen and survived for 15 weeks under atmospheric conditions. Spores tolerated heat stress at 70 °C, but not at 80 °C. An in silico analysis of the conservation of potential sporulation signature genes revealed that the majority of human gut butyrate-producing bacteria were classified as potential spore formers. Comparative genomics revealed that three spore-forming Anaerostipes spp. specifically possessed the spore formation-related genes of bkdR, sodA, and splB, which may be key genes for different sporulation properties in Anaerostipes spp.

CONCLUSIONS

The present study demonstrated the enhanced stress tolerance of butyrate producing Anaerostipes spp. for future probiotic application. Presence of specific gene(s) are possibly keys for sporulation in Anaerostipes spp.

Metagenome and metabolome insights into the energy compensation and exogenous toxin degradation of gut microbiota in high-altitude rhesus macaques (Macaca mulatta)

There have been many reports on the genetic mechanism in rhesus macaques (RMs) for environmental adaptation to high altitudes, but the synergistic involvement of gut microbiota in this adaptation remains unclear. Here we performed fecal metagenomic and metabolomic studies on samples from high- and low-altitude populations to assess the synergistic role of gut microbiota in the adaptation of RMs to high-altitude environments. Microbiota taxonomic annotation yielded 7471 microbiota species. There were 37 bacterial species whose abundance was significantly enriched in the high-altitude populations, 16 of which were previously reported to be related to the host's dietary digestion and energy metabolism. Further functional gene enrichment found a stronger potential for gut microbiota to synthesize energy substrate acetyl-CoA using CO₂ and energy substrate pyruvate using oxaloacetate, as well as a stronger potential to transform acetyl-CoA to energy substrate acetate in high-altitude populations. Interestingly, there were no apparent differences between low-altitude and high-altitude populations in terms of genes enriched in the main pathways by which the microbiota consumed the three energy substrates, and none of the three energy substrates were detected in the fecal metabolites. These results strongly suggest that gut microbiota plays an important energy compensatory role that helps RMs to adapt to high-altitude environments. Further functional enrichment after metabolite source analysis indicated the abundance of metabolites related to the degradation of exogenous toxins was also significantly higher in high-altitude populations, which suggested a contributory role of gut microbiota to the degradation of exogenous toxins in wild RMs adapted to high-altitude environments.

Butyrate producers, "The Sentinel of Gut": Their intestinal significance with and beyond butyrate, and prospective use as microbial therapeutics

Gut-microbial butyrate is a short-chain fatty acid (SCFA) of significant physiological importance than the other major SCFAs (acetate and propionate). Most butyrate producers belong to the Clostridium cluster of the phylum Firmicutes, such as Faecalibacterium, Roseburia, Eubacterium, Anaerostipes, Coprococcus, Subdoligranulum, and Anaerobutyricum. They metabolize carbohydrates via the butyryl-CoA: acetate CoA-transferase pathway and butyrate kinase terminal enzymes to produce most of butyrate. Although, in minor fractions, amino acids can also be utilized to generate butyrate via glutamate and lysine pathways. Butyrogenic microbes play a vital role in various gut-associated metabolisms. Butyrate is used by colonocytes to generate energy, stabilizes hypoxia-inducible factor to maintain the anaerobic environment in the gut, maintains gut barrier integrity by regulating Claudin-1 and synaptopodin expression, limits pro-inflammatory cytokines (IL-6, IL-12), and inhibits oncogenic pathways (Akt/ERK, Wnt, and TGF-β signaling). Colonic butyrate producers shape the gut microbial community by secreting various anti-microbial substances, such as cathelicidins, reuterin, and β-defensin-1, and maintain gut homeostasis by releasing anti-inflammatory molecules, such as IgA, vitamin B, and microbial anti-inflammatory molecules. Additionally, butyrate producers, such as Roseburia, produce anti-carcinogenic metabolites, such as shikimic acid and a precursor of conjugated linoleic acid. In this review, we summarized the significance of butyrate, critically examined the role and relevance of butyrate producers, and contextualized their importance as microbial therapeutics.

Prebiotic Isomaltooligosaccharide Provides an Advantageous Fitness to the Probiotic Bacillus subtilis CU1

Bacillus subtilis CU1 is a probiotic strain with beneficial effects on immune health in elderly subjects and diarrhea. Commercialized under spore form, new strategies to improve the germination, fitness and beneficial effects of the probiotic once in the gut have to be explored. For this purpose, functional food ingredients, such as isomaltooligosaccharides (IMOSs), could improve the fitness of Bacillus probiotics. IMOSs are composed of α(1 → 6)- and α(1 → 4)-linked oligosaccharides and are partially indigestible. Dietary IMOSs stimulate beneficial members of intestinal microbiota, but the effect of a combination of IMOSs with probiotics, such as B. subtilis CU1, is unknown. In this study, we evaluate the potential effect of IMOSs in B. subtilis CU1 and identify the metabolic pathways involved. The biochemical analysis of the commercial IMOSs highlights a degree of polymerization (DP) comprised between 1 and 29. The metabolism of IMOSs in CU1 was attributed to an α-glucosidase, secreted in the extracellular compartment one hundred times more than with glucose, and which seems to hydrolyze high DP IMOSs into shorter oligosaccharides (DP1, DP2 and DP3) in the culture medium. Proteomic analysis of CU1 after growth on IMOSs showed a reshaping of B. subtilis CU1 metabolism and functions, associated with a decreased production of lactic acid and acetic acid by two times. Moreover, we show for the first time that IMOSs could improve the germination of a Bacillus probiotic in the presence of bile salts in vitro, with an 8 h reduced lag-time when compared to a glucose substrate. Moreover, bacterial concentration (CFU/mL) was increased by about 1 log in IMOS liquid cultures after 48 h when compared to glucose. In conclusion, the use of IMOSs in association with probiotic B. subtilis CU1 in a synbiotic product could improve the fitness and benefits of the probiotic.