Profiling of the intestinal community of Clostridia: taxonomy and evolutionary analysis

Flavonoid-converting capabilities of Clostridium butyricum

Clostridium butyricum inhabits various anoxic environments, including soil and the human gut. Here, this common bacterium comes into contact with abundant plant-derived flavonoids. Metabolization of these bioactive polyphenols has been studied in recent years, particularly focusing on gut bacteria due to the proposed health-promoting properties of these dietary constituents. Based on an initial report in 1997 on eriodictyol degradation (Miyake et al. 1997, J Agric Food Chem, 45:3738-3742), the present study systematically investigated C. butyricum for its ability to convert a set of structurally diverse flavonoids. Incubation experiments revealed that C. butyricum deglycosylated flavonoid O-glucosides but only when glucose was absent. Moreover, aglycone members of flavone, flavanone, dihydrochalcone, and flavanonol subclasses were degraded. The C-ring cleavage of the flavanones, naringenin and eriodictyol, was stereospecific and finally resulted in formation of the corresponding hydroxyphenylpropionic acids. Stereospecific C-ring cleavage of the flavanonol taxifolin led to taxifolin dihydrochalcone. C. butyricum did neither cleave flavonols and isoflavones nor catalyze de-rhamnosylation, demethylation, or dehydroxylation of flavonoids. Genes encoding potential flavonoid-metabolizing enzymes were detected in the C. butyricum genome. Overall, these findings indicate that C. butyricum utilizes flavonoids as alternative substrates and, as observed for the dihydrochalcone phloretin, can eliminate growth-inhibiting flavonoids through degradation. KEY POINTS: • Clostridium butyricum deglycosylated flavonoid O-glucosides. • Clostridium butyricum converted members of several flavonoid subclasses. • Potential flavonoid-metabolizing enzymes are encoded in the C. butyricum genome.

Molecular epidemiology of Eimeria spp. parasites and the faecal microbiome of Indiana bats (Myotis sodalis): a non-invasive, multiplex metabarcode survey of an endangered species

Assessing individual and population health in endangered wildlife poses unique challenges due to the lack of an adequate baseline and ethical constraints on invasive sampling. For endangered bats, minimally invasive samples like guano can often be the ethical and technical limit for studies of pathogens and the microbiome. In this study, we use multiplex metabarcode sequencing to describe the faecal microbiome and parasites of 56 Indiana bats (Myotis sodalis). We show evidence of a high prevalence of Eimeria spp. protozoan parasite and characterize associations between infection and changes to the faecal microbiome. We identify a strong and significant enrichment of Clostridium species in Eimeria-positive bats, including isolates related to Clostridium perfringens.

Genomic and functional analysis of the mucinolytic species Clostridium celatum, Clostridium tertium, and Paraclostridium bifermentans

Mucins are large glycoproteins whose degradation requires the expression of several glycosil hydrolases to catalyze the cleavage of the oligosaccharide chains and release monosaccharides that can be assimilated. In this study, we present a characterization on the strains Clostridium celatum WC0700, Clostridium tertium WC0709, and Paraclostridium bifermentans WC0705. These three strains were previously isolated from enrichment cultures on mucin of fecal samples from healthy subjects and can use mucin as sole carbon and nitrogen source. Genome analysis and in vitro functional analysis of these strains elucidated their physiological and biochemical features. C. celatum WC0700 harbored the highest number of glycosyl hydrolases specific for mucin degradation, while P. bifermentans WC0705 had the least. These predicted differences were confirmed growing the strains on 5 mucin-decorating monosaccharides (L-fucose, N-Acetylneuraminic acid, galactose, N-acetylgalactosamine, and N-acetylglucosamine) as only source of carbon. Fermenting mucin, they all produced formic, acetic, propionic, butyric, isovaleric, and lactic acids, and ethanol; acetic acid was the main primary metabolite. Further catabolic capabilities were investigated, as well as antibiotic susceptibility, biofilm formation, tolerance to oxygen and temperature. The potential pathogenicity of the strains was evaluated through in silico research of virulence factors. The merge between comparative and functional genomics and biochemical/physiological characterization provided a comprehensive view of these mucin degraders, reassuring on the safety of these species and leaving ample scope for deeper investigations on the relationship with the host and for assessing if some relevant health-promoting effect could be ascribed to these SCFA producing species.

Breastfeeding and the major fermentation metabolite lactate determine occurrence of Peptostreptococcaceae in infant feces

Previous studies indicated an intrinsic relationship between infant diet, intestinal microbiota composition and fermentation activity with a strong focus on the role of breastfeeding on microbiota composition. Yet, microbially formed short-chain fatty acids acetate, propionate and butyrate and other fermentation metabolites such as lactate not only act as substrate for bacterial cross-feeding and as mediators in microbe-host interactions but also confer antimicrobial activity, which has received considerably less attention in the past research. It was the aim of this study to investigate the nutritional-microbial interactions that contribute to the development of infant gut microbiota with a focus on human milk oligosaccharide (HMO) fermentation. Infant fecal microbiota composition, fermentation metabolites and milk composition were analyzed from 69 mother-infant pairs of the Swiss birth cohort Childhood AlleRgy nutrition and Environment (CARE) at three time points depending on breastfeeding status defined at the age of 4 months, using quantitative microbiota profiling, HPLC-RI and 1H-NMR. We conducted in vitro fermentations in the presence of HMO fermentation metabolites and determined the antimicrobial activity of lactate and acetate against major Clostridiaceae and Peptostreptococcaceae representatives. Our data show that fucosyllactose represented 90% of the HMOs present in breast milk at 1- and 3-months post-partum with fecal accumulation of fucose, 1,2-propanediol and lactate indicating fermentation of HMOs that is likely driven by Bifidobacterium. Concurrently, there was a significantly lower absolute abundance of Peptostreptococcaceae in feces of exclusively breastfed infants at 3 months. In vitro, lactate inhibited strains of Peptostreptococcaceae. Taken together, this study not only identified breastfeeding dependent fecal microbiota and metabolite profiles but suggests that HMO-derived fermentation metabolites might exert an inhibitory effect against selected gut microbes.