Draft genome sequence of the mucin degrader clostridium tertium wc0709

The draft genome sequence of Clostridium tertium WC0709, a gut bacterium able to use mucin in pure culture as the sole carbon and nitrogen source, is presented here. The genome sequence of C. tertium will provide valuable references for comparative genome analysis and for studying the relationship with the host

Identification of mucin degraders of the human gut microbiota

Mucins are large glycoproteins consisting of approximately 80% of hetero-oligosaccharides. Gut mucin degraders of healthy subjects were investigated, through a culture dependent and independent approach. The faeces of five healthy adults were subjected to three steps of anaerobic enrichment in a medium with sole mucins as carbon and nitrogen sources. The bacterial community was compared before and after the enrichment by 16S rRNA gene profiling. Bacteria capable of fermenting sugars, such as Anaerotruncus, Holdemania, and Enterococcaceae likely took advantage of the carbohydrate chains. Escherichia coli and Enterobacteriaceae, Peptococcales, the Coriobacteriale Eggerthella, and a variety of Clostridia such as Oscillospiraceae, Anaerotruncus, and Lachnoclostridium, significantly increased and likely participated to the degradation of the protein backbone of mucin. The affinity of E. coli and Enterobacteriaceae for mucin may facilitate the access to the gut mucosa, promoting gut barrier damage and triggering systemic inflammatory responses. Only three species of strict anaerobes able to grow on mucin were isolated from the enrichments of five different microbiota: Clostridium disporicum, Clostridium tertium, and Paraclostridium benzoelyticum. The limited number of species isolated confirms that in the gut the degradation of these glycoproteins results from cooperation and cross-feeding among several species exhibiting different metabolic capabilities

Hemp Biomass Pretreatment and Fermentation with non- Saccharomyces Yeasts: Xylose Valorization to Xylitol

Hemp hurds are the main byproduct from hemp fibers supply chain and they could represent valuable feedstock of lignocellulosic biomass for biorefineries. The industrial hemp variety "Carmagnola", is characterized by low amounts of ash and high amount of carbohydrates. Alpha-cellulose (44% w/w), hemicellulose (25%), and lignin (23%) were fractionated using an organosolv pretreatment. The enzymatic hydrolysis of the cellulose fraction yielded up to 60% of glucose, that can easily find application as substrate for industrial fermentations. On the other hand, the black liquor originating from hemicellulose contains mainly xylose and minor amounts of other sugars. In the perspective of finding an application of black liquor, 50 yeasts belonging to 24 ascomycetous species were screened both in aerobiosis and anaerobiosis for the production of ethanol and the sugar alcohols xylitol and arabitol from xylose. Pichia fermentans WC 1507, Wickerhamomyces anomalus WC 1501, and Kluyveromyces bacillosporus WC 1404 were found to consume xylose, yielding xylitol in aerobic conditions. In particular, aerobic flask cultures of P. fermentans WC 1507 containing 120 g/L xylose showed the highest xylitol production values, yielding 63.5 g/L xylitol with a YP/S of 71.5%. Black liquor, exploited as a carbon source, has been successfully utilized by the three selected yeast strains at a concentration of 20 g/L in the culture medium, resulting in comparable or higher yields of biomass and xylitol compared to the medium containing pure xylose. A higher concentration of black liquor in the culture medium (to reach 120 g/l of xylose) has determined an inhibition of the growth of yeasts indicating the need for treatments for the removal of inhibitors. These preliminary results can be considered promising for the microbial valorization of lignocellulosic hemp feedstock toward the production of xylitol

Multivariate Analysis in Microbiome Description: Correlation of Human Gut Protein Degraders, Metabolites, and Predicted Metabolic Functions

Protein catabolism by intestinal bacteria is infamous for releasing many harmful compounds, negatively affecting the health status, both locally and systemically. In a previous study, we enriched in protein degraders the fecal microbiota of five subjects, utilizing a medium containing protein and peptides as sole fermentable substrates and we monitored their evolution by 16S rRNA gene profiling. In the present study, we fused the microbiome data and the data obtained by the analysis of the volatile organic compounds (VOCs) in the headspace of the cultures. Then, we utilized ANOVA simultaneous component analysis (ASCA) to establish a relationship between metabolites and bacteria. In particular, ASCA allowed to separately assess the effect of subject, time, inoculum concentration, and their binary interactions on both microbiome and volatilome data. All the ASCA submodels pointed out a consistent association between indole and Escherichia–Shigella, and the relationship of butyric, 3-methyl butanoic, and benzenepropanoic acids with some bacterial taxa that were major determinants of cultures at 6 h, such as Lachnoclostridiaceae (Lachnoclostridium), Clostridiaceae (Clostridium sensu stricto), and Sutterellaceae (Sutterella and Parasutterella). The metagenome reconstruction with PICRUSt2 and its functional annotation indicated that enrichment in a protein-based medium affected the richness and diversity of functional profiles, in the face of a decrease of richness and evenness of the microbial community. Linear discriminant analysis (LDA) effect size indicated a positive differential abundance (p < 0.05) for the modules of amino acid catabolism that may be at the basis of the changes of VOC profile. In particular, predicted genes encoding functions belonging to the superpathways of ornithine, arginine, and putrescine transformation to GABA and eventually to succinyl-CoA, of methionine degradation, and various routes of breakdown of aromatic compounds yielding succinyl-CoA or acetyl-CoA became significantly more abundant in the metagenome of the bacterial community

Potential of wickerhamomyces anomalus in glycerol valorization

Five-carbons polyalcohols, such as xylitol and arabitol, and microbial oils are important targets for biotechnological industries. Polyalcohols can find application as low-calories sweeteners and as building block in the synthesis of valuable compounds, while lipids are interesting for both biofuel and food industry. The osmophilic yeast Wickerhamomyces anomalus WC 1501 was preliminary known to produce arabitol from glycerol. Production kinetics were investigated in this study. Production was not growth-associated and occurred during a nitrogen-limited stationary phase, in presence of an excess of carbon source. Typical bioreactor batch cultures, carried out with 160 g/L glycerol, yielded 16.0 g/L arabitol in 160 h. A fed-batch process was developed, in which growth is carried out batchwise in a balanced medium containing 20 g/L glycerol, and arabitol production is induced at the entrance into the stationary phase with a pulse of concentrated glycerol to provide the remaining 140 g/L carbon source. At the end of the process 18.0 g/L arabitol were generated. Under these conditions, the yeast also accumulated intracellular triacylglycerols, with fatty acids of 16-18 carbons bearing 0 to 2 unsaturations, reaching up the 23% of biomass dry weight. Therefore, W. anomalus WC 1501 is a good candidate for the development of a fermentative process yielding arabitol and has potential also as oleaginous yeast for producing lipids, further improving the interest in this strain for glycerol biorefinery. The utilization of a fed-batch process allows to carry out distinct growth and production phases and thus allows the optimization of both phases separately, in order to achieve the highest concentration of catalytic biomass during growth and the maximum efficiency during production. This strain deserves further investigation to better exploit its biotechnological potential in the valorization of glycerol

Vaginal and anal microbiome during chlamydia trachomatis infections

Background. Chlamydia trachomatis (CT) is the agent of the most common bacterial sexually transmitted infection worldwide, with a significant impact on women’s health. Despite the increasing number of studies about the vaginal microbiome in women with CT infections, information about the composition of the anal microbiome is still lacking. Here, we assessed the bacterial community profiles of vaginal and anal ecosystems associated or not with CT infection in a cohort of Caucasian young women. Methods. A total of 26 women, including 10 with a contemporary vaginal and anorectal CT infection, were enrolled. Composition of vaginal and anal microbiome was studied by 16S rRNA gene profiling. Co-occurrence networks of bacterial communities and metagenome metabolic functions were determined. Results. In case of CT infection, both vaginal and anal environments were characterized by a degree of dysbiosis. Indeed, the vaginal microbiome of CT-positive women were depleted in lactobacilli, with a significant increase in dysbiosis-associated bacteria (e.g., Sneathia, Parvimonas, Megasphaera), whereas the anal microbiota of CT-infected women was characterized by higher levels of Parvimonas and Pseudomonas and lower levels of Escherichia. Interestingly, the microbiome of anus and vagina had numerous bacterial taxa in common, reflecting a significant microbial ‘sharing’ between the two sites. In the vaginal environment, CT positively correlated with Ezakiella spp. while Gardnerella vaginalis co-occurred with several dysbiosis-related microbes, regardless of CT vaginal infection. The vaginal microbiome of CT-positive females exhibited a higher involvement of chorismate and aromatic amino acid biosynthesis, as well as an increase in mixed acid fermentation. Conclusions. These data could be useful to set up new diagnostic/prognostic tools, offering new perspectives for the control of chlamydial infections

Phenotypic Traits and Immunomodulatory Properties of Leuconostoc carnosum Isolated From Meat Products

Twelve strains of Leuconostoc carnosum from meat products were investigated in terms of biochemical, physiological, and functional properties. The spectrum of sugars fermented by L. carnosum strains was limited to few mono- and disaccharides, consistently with the natural habitats of the species, including meat and fermented vegetables. The strains were able to grow from 4 to 37C with an optimum of approximately 32.5C. The ability to grow at temperatures compatible with refrigeration and in presence of up to 60 g/L NaCl explains the high loads of L. carnosum frequently described in many meat-based products. Six strains produced exopolysaccharides, causing a ropy phenotype of colonies, according to the potential involvement on L. carnosum in the appearance of slime in packed meat products. On the other side, the study provides evidence of a potential protective role of L. carnosum WC0321 and L. carnosum WC0323 against Listeria monocytogenes, consistently with the presence in these strains of the genes encoding leucocin B. Some meat-based products intended to be consumed without cooking may harbor up to 108 CFU/g of L. carnosum; therefore, we investigated the potential impact of this load on health. No strains survived the treatment with simulated gastric juice. Three selected strains were challenged for the capability to colonize a mouse model and their immunomodulatory properties were investigated. The strains did not colonize the intestine of mice during 10 days of daily dietary administration. Intriguingly, despite the loss of viability during the gastrointestinal transit, the strains exhibited different immunomodulatory effect on the maturation of dendritic cells in vivo, the extent of which correlated to the production of exopolysaccharides. The ability to stimulate the mucosal associated immune system in such probiotic-like manner, the general absence of antibiotic resistance genes, and the lack of the biosynthetic pathways for biogenic amines should reassure on the safety of this species, with potential for exploitation of selected starters

Riboflavin Biosynthesis and Overproduction by a Derivative of the Human Gut Commensal Bifidobacterium longum subsp. infantis ATCC 15697

Riboflavin or vitamin B2 is the precursor of the essential coenzymes flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD). Despite increased interest in microbial synthesis of this water-soluble vitamin, the metabolic pathway for riboflavin biosynthesis has been characterized in just a handful of bacteria. Here, comparative genome analysis identified the genes involved in the de novo biosynthetic pathway of riboflavin in certain bifidobacterial species, including the human gut commensal Bifidobacterium longum subsp. infantis (B. infantis) ATCC 15697. Using comparative genomics and phylogenomic analysis, we investigated the evolutionary acquisition route of the riboflavin biosynthesis or rib gene cluster in Bifidobacterium and the distribution of riboflavin biosynthesis-associated genes across the genus. Using B. infantis ATCC 15697 as model organism for this pathway, we isolated spontaneous riboflavin overproducers, which had lost transcriptional regulation of the genes required for riboflavin biosynthesis. Among them, one mutant was shown to allow riboflavin release into the medium to a concentration of 60.8 ng mL–1. This mutant increased vitamin B2 concentration in a fecal fermentation system, thus providing promising data for application of this isolate as a functional food ingredient

Antibiotic resistance, virulence factors, phenotyping, and genotyping of non\u2013escherichia coli enterobacterales from the gut microbiota of healthy subjects

Non-Escherichia coli Enterobacterales (NECE) can colonize the human gut and may present virulence determinants and phenotypes that represent severe heath concerns. Most information is available for virulent NECE strains, isolated from patients with an ongoing infection, while the commensal NECE population of healthy subjects is understudied. In this study, 32 NECE strains were isolated from the feces of 20 healthy adults. 16S rRNA gene sequencing and mass spectrometry attributed the isolates to Klebsiella pneumoniae, Klebsiella oxytoca, Enterobacter cloacae, Enterobacter aerogenes, Enterobacter kobei, Citrobacter freundii, Citrobacter amalonaticus, Cronobacter sp., and Hafnia alvei, Morganella morganii, and Serratia liquefaciens. Multiplex PCR revealed that K. pneumoniae harbored virulence genes for adhesins (mrkD, ycfM, and kpn) and enterobactin (entB) and, in one case, also for yersiniabactin (ybtS, irp1, irp2, and fyuA). Virulence genes were less numerous in the other NECE species. Biofilm formation was spread across all the species, while curli and cellulose were mainly produced by Citrobacter and Enterobacter. Among the most common antibiotics, amoxicillin-clavulanic acid was the sole against which resistance was observed, only Klebsiella strains being susceptible. The NECE inhabiting the intestine of healthy subjects have traits that may pose a health threat, taking into account the possibility of horizontal gene transfer