Genomic insights from Paraclostridium bifermentans HD0315_2: General features and pathogenic potential

Assessment of Microbial and Heavy Metal Contamination of Natural Sheep Casings from Different Geographic Regions

Natural casings are integral components in the production of various meat products, including sausages, and their quality and safety have to be controlled to eliminate any risks to consumers' health. A total of 35 samples of salted natural sheep casings from Turkey, Iran, China, Mongolia, Pakistan, New Zealand, the United Kingdom, and Belgium were tested for microbial contamination and the concentrations of potentially toxic heavy metals. The mean log values of microbial counts were determined at 3.45 ± 0.44 log CFU/g for aerobic mesophilic bacteria, 0.5 ± 0.43 log CFU/g for anaerobic sulfide-reducing bacteria, and 1.24 ± 0.63 log CFU/g for coagulase-positive staphylococci. Typical or suspected colonies of Salmonella spp., E. coli, and Listeria spp. were not identified on selective and differential agar. The examined casings were contaminated mainly with lead (0.077 ± 0.045 mg/kg), followed by arsenic (0.036 ± 0.029 mg/kg) and cadmium (0.009 ± 0.008 mg/kg). The concentrations of mercury in all samples were below the limit of quantification. The study demonstrated that the quality and safety of natural casings were not affected by their region of origin and that microbial contamination was not correlated with heavy metal concentrations.

Effects of Dietary Inclusion of Enzymatically Hydrolyzed Compound Soy Protein on the Growth Performance and Intestinal Health of Juvenile American Eels (Anguilla rostrata)

The enzymatic hydrolysis of soybeans could enhance their application as an ingredient and alternative to fishmeal in aquafeeds. Here, a 10-week feeding trial was conducted to evaluate the impacts of different dietary inclusion levels of enzymatically hydrolyzed compound soy protein (EHCS) on the growth performance and intestinal health of juvenile American eels (Anguilla rostrata). Five experimental diets were formulated with graded EHCS inclusion levels at 0% (EHCS0), 8% (EHCS8), 16% (EHCS16), 24% (EHCS24), and 32% (EHCS32). Each diet was randomly assigned to four replicate tanks. The results showed that eels fed the EHCS8 diet exhibited superior growth performance, decreased serum lipid content, and increased immunity compared to those fed the EHCS0 diet. Eels fed the EHCS8 diet also displayed improved intestinal histology, enhanced antioxidant capacity and balance of intestinal microbiota as well as an enhanced proliferation of probiotics compared to those receiving the EHCS0 diet. Compared with eels fed the EHCS0 diet, those fed the EHCS16 diet exhibited comparable growth performance and values for the aforementioned markers. The quadratic regression analysis of weight gain rate and feed efficiency against the dietary EHCS inclusion levels determined the maximum levels of dietary EHCS inclusion for American eels range from 17.59% to 17.77%.

Short-chain fatty acid-producing bacterial strains attenuate experimental ulcerative colitis by promoting M2 macrophage polarization via JAK/STAT3/FOXO3 axis inactivation

BACKGROUND

Patients with inflammatory bowel disease (IBD), dysbiosis, and immunosuppression who receive fecal microbiota transplantation (FMT) from healthy donors are at an increased risk of developing bacteremia. This study investigates the efficacy of a mixture of seven short-chain fatty acid (SCFA)-producing bacterial strains (7-mix), the resulting culture supernatant mixture (mix-sup), and FMT for treating experimental ulcerative colitis (UC) and evaluates underlying mechanisms.

METHODS

Utilizing culturomics, we isolated and cultured SCFA-producing bacteria from the stool of healthy donors. We used a mouse model of acute UC induced by dextran sulfate sodium (DSS) to assess the effects of 7-mix, mix-sup, and FMT on intestinal inflammation and barrier function, microbial abundance and diversity, and gut macrophage polarization by flow cytometry, immunohistochemistry, 16S rRNA gene sequencing, and transwell assays.

RESULTS

The abundance of several SCFA-producing bacterial taxa decreased in patients with UC. Seven-mix and mix-sup suppressed the inflammatory response and enhanced intestinal mucosal barrier function in the mouse model of UC to an extent similar to or superior to that of FMT. Moreover, 7-mix and mix-sup increased the abundance of SCFA-producing bacteria and SCFA concentrations in colitic mice. The effects of these interventions on the inflammatory response and gut barrier function were mediated by JAK/STAT3/FOXO3 axis inactivation in macrophages by inducing M2 macrophage polarization in vivo and in vitro.

CONCLUSIONS

Our approach provides new opportunities to rationally harness live gut probiotic strains and metabolites to reduce intestinal inflammation, restore gut microbial composition, and expedite the development of safe and effective treatments for IBD.

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.

Populational genomic insights of Paraclostridium bifermentans as an emerging human pathogen

Paraclostridium bifermentans (P.b) is an emerging human pathogen that is phylogenomically close to Paeniclostridium sordellii (P.s), while their populational genomic features and virulence capacity remain understudied. Here, we performed comparative genomic analyses of P.b and compared their pan-genomic features and virulence coding profiles to those of P.s. Our results revealed that P.b has a more plastic pangenome, a larger genome size, and a higher GC content than P.s. Interestingly, the P.b and P.s share similar core-genomic functions, but P.b encodes more functions in nutrient metabolism and energy conversion and fewer functions in host defense in their accessory-genomes. The P.b may initiate extracellular infection processes similar to those of P.s and Clostridium perfringens by encoding three toxin homologs (i.e., microbial collagenase, thiol-activated cytolysin, phospholipase C, which are involved in extracellular matrices degradation and membrane damaging) in their core-genomes. However, P.b is less toxic than the P.s by encoding fewer secretion toxins in the core-genome and fewer lethal toxins in the accessory-genome. Notably, P.b carries more toxins genes in their accessory-genomes, particularly those of plasmid origin. Moreover, three within-species and highly conserved plasmid groups, encoding virulence, gene acquisition, and adaptation, were carried by 25-33% of P.b strains and clustered by isolation source rather than geography. This study characterized the pan-genomic virulence features of P.b for the first time, and revealed that P. bifermentans is an emerging pathogen that can threaten human health in many aspects, emphasizing the importance of phenotypic and genomic characterizations of in situ clinical isolates.