In silico RFLP Analysis of 16S rRNA Genes: A Helpful Application for Distinguishing Bifidobacteria from Human and Animal Source

Bifidobacterial species are widespread in gastrointestinal tracts of mammalian and other animals; they can be found in extra body environment only after a fecal contamination or human intentional addition (as the case of probiotics). Interestingly their occurrence is strictly linked to their hosts with a clear demarcation between animal and human species. PCR-restriction fragment length polymorphism (PCR-RFLP) on the 16S rRNA gene, using Alul, and TaqI restriction enzymes, have been utilized to distinguish the animal or human source of 64 strains belonging to 13 Bifidobacterium species (Delcenserie et al. [15]). Our aim was to test this method updating an in silico restriction analysis on the available 16S rRNA gene sequences of all 55 currently described taxa of Bifidobacterium genus. Our results confirmed the reliability of this method, optimized with the use of three restriction enzymes: Alul, TaqI and MaeIII, as a fast and simple strategy to determine the origin (human or animal) of bifidobacteria. Interestingly, the bifidobacterial species recently isolated from non-human primates cluster in the group of animal source except the bifidobacterial species isolated from higher non-human primates closest to humans such as apes (chimpanzee, orangutan and gorilla) that clusters with human group. Moreover, B. minimum, B. subtile and B. mongoliense isolated only from extrabody environment of which the source is unknown clustered with animal species. The in silico RFLP-PCR confirmed its powerful ability to attribute the primary source of occurrence (human or animal) for bifidobacterial species to the human or animal habitat

Host-Diet Effect on the Metabolism of Bifidobacterium

Bifidobacterium has a diverse host range and shows several beneficial properties to the hosts. Many species should have co-evolved with their hosts, but the phylogeny of Bifidobacterium is dissimilar to that of host animals. The discrepancy could be linked to the niche-specific evolution due to hosts’ dietary carbohydrates. We investigated the relationship between bifidobacteria and their host diet using a comparative genomics approach. Since carbohydrates are the main class of nutrients for bifidobacterial growth, we examined the distribution of carbohydrate-active enzymes, in particular glycoside hydrolases (GHs) that metabolize unique oligosaccharides. When bifidobacterial species are classified by their distribution of GH genes, five groups arose according to their hosts’ feeding behavior. The distribution of GH genes was only weakly associated with the phylogeny of the host animals or with genomic features such as genome size. Thus, the hosts’ dietary pattern is the key determinant of the distribution and evolution of GH genes

Bifidobacterium mellis sp. nov., isolated from the honey stomach of the honey bee Apis mellifera

: A novel Bifidobacterium strain, Bin7NT, was isolated from the honey stomach of the honey bee Apis mellifera. Cells are Gram-positive, non-motile, non-sporulating, facultative anaerobic and fructose 6-phosphate phosphoketolase-positive. Their optimal growth is at 37 °C in anaerobiosis in MRS (De Man, Rogosa and Sharpe) added with cysteine. The honey bee microbiota was composed of several phylotypes of Bifidobacterium and Lactobacillus. Comparative analysis of 16S rRNA gene sequence similarity revealed that strain Bin7NT grouped with Bifidobacterium species originating from honey bees and was closely related to Bifidobacterium asteroides DSM 20089T (99.67 % similarity). However, the highest average nucleotide identity and digital DNA-DNA hybridization values of 94.88 and 60.6 %, respectively, were obtained with Bifidobacterium choladohabitans JCM 34586T. The DNA G+C content of the type strain is 60.8 mol%. The cell-wall peptidoglycan is of the A4β l-Orn-d-Asp type. The main cellular fatty acids of strain Bin7NT are C18 : 1 ω9c, C16 : 0, C18 : 1 ω7c and C18 : 0. Phenotypic characterization and genotyping based on the genome sequences clearly show that this strain is distinct from the type strains of the so far recognized Bifidobacterium species. Thus, Bifidobacterium mellis sp. nov. (Bin7NT=DSM 29108T=CCUG 66113T) is proposed as novel Bifidobacterium species

Occurrence of Bifidobacteriaceae in human hypochlorhydria stomach

open7noBackground: The human stomach, when healthy, is not a suitable host for microorganisms, but in pathological conditions such as gastritis, when gastric acid secretion is impaired, microbial overgrowth can be observed. Apart from Helicobacter pylori, the composition of microbiota, resident or exogenously introduced during neutral/high pH conditions, has not been investigated thoroughly. Thus, it is possible that Bifidobacteriaceae, important autochthonous and beneficial bacteria of human gastrointestinal microbiota, could over-colonize the stomach of hypochlorhydria patients suffering from autoimmune atrophic gastritis (AAG) or omeprazoletreated (OME) gastritis. This prompted us to characterize the Bifidobacteriaceae in such patients’ gastric microbiota and to study its abnormal colonization. Methods: Samples of gastric juices, and antrum and corpus mucosa from 23 hypochlorhydria patients (13 AAG and 10 OME) and from 10 control volunteers with base-line normochlorhydria, were cultivated in Brain Heart Infusion (BHI) and selective Bifidobacterium-Tryptone-Phytone-Yeast extract (Bif-TPY) media. The isolates were characterized by the fructose-6-phosphate phosphoketolase (F6PPK) test, electrophoresis of cellular proteins, the fermentation test, guanine-cytosine% DNA content, and DNADNA hybridization. Negative F6PPK isolates were characterized by order-specific polymerase chain reaction (PCR). Results: A total of 125 isolates, assigned to the Bifidobacteriaceae family on the basis of their morphology, were obtained from AAG and OME patients, but not from normal subjects. Of these isolates, 55 were assigned to the Bifidobacteriaceae family on the basis of their fructose-6-phosphoketolase (PPK) activity, PPK being the key taxonomic enzyme of this family. The remaining 70 isolates, which were PPK-negative, were attributed to the Actinomycetales order following specific primer PCR analysis. We observed a significantly higher abundance of Bifidobacteriaceae (Bifidobacterium dentium, Scardovia inopinata, and Parascardovia denticolens) in OME group than the AAG group. Furthermore, the Actinomycetales distribution was homogeneous for both hypochlorhydria patient groups. Conclusions: This study suggests that the Bifidobacteriaceae species, typically found in the oral cavity, readily colonizes the hypochlorhydria stomach of OME patients. The clinical relevance and the mechanism underlying this Bifidobacteriaceae presence in OME gastritis requires further functional studies.openPaola Mattarelli; Giovanni Brandi; Carlo Calabrese; Fabio Fornari; Gian Maria Prati; Bruno Biavati; Barbara SgorbatiPaola Mattarelli; Giovanni Brandi; Carlo Calabrese; Fabio Fornari; Gian Maria Prati; Bruno Biavati; Barbara Sgorbat

International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Bifidobacterium, Lactobacillus and related organisms. Minutes of the closed meeting by videoconference, 3 September 2020

International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Bifidobacterium, Lactobacillus and related organisms. Minutes of the closed meeting by videoconference, 3 September 202

Identification of species belonging to the Bifidobacterium genus by PCR-RFLP analysis of a hsp60 gene fragment

Abstract BACKGROUND: Bifidobacterium represents one of the largest genus within the Actinobacteria, and includes at present 32 species. These species share a high sequence homology of 16S rDNA and several molecular techniques already applied to discriminate among them give ambiguous results.The slightly higher variability of the hsp60 gene sequences with respect to the 16S rRNA sequences offers better opportunities to design or develop molecular assays, allowing identification and differentiation of closely related species. hsp60 can be considered an excellent additional marker for inferring the taxonomy of the members of Bifidobacterium genus. RESULTS: This work illustrates a simple and cheap molecular tool for the identification of Bifidobacterium species. The hsp60 universal primers were used in a simple PCR procedure for the direct amplification of 590 bp of the hsp60 sequence. The in silico restriction analysis of bifidobacterial hsp60 partial sequences allowed the identification of a single endonuclease (HaeIII) able to provide different PCR-restriction fragment length polymorphism (RFLP) patterns in the Bifidobacterium spp. type strains evaluated. The electrophoretic analyses allowed to confirm the different RFLP patterns. CONCLUSIONS: The developed PCR-RFLP technique resulted in efficient discrimination of the tested species and subspecies and allowed the construction of a dichotomous key in order to differentiate the most widely distributed Bifidobacterium species as well as the subspecies belonging to B. pseudolongum and B. animalis

Gut microbiota profiles and characterization of cultivable fungal isolates in IBS patients

Studies so far conducted on irritable bowel syndrome (IBS) have been focused mainly on the role of gut bacterial dysbiosis in modulating the intestinal permeability, inflammation, and motility, with consequences on the quality of life. Limited evidences showed a potential involvement of gut fungal communities. Here, the gut bacterial and fungal microbiota of a cohort of IBS patients have been characterized and compared with that of healthy subjects (HS). The IBS microbial community structure differed significantly compared to HS. In particular, we observed an enrichment of bacterial taxa involved in gut inflammation, such as Enterobacteriaceae, Streptococcus, Fusobacteria, Gemella, and Rothia, as well as depletion of health-promoting bacterial genera, such as Roseburia and Faecalibacterium. Gut microbial profiles in IBS patients differed also in accordance with constipation. Sequence analysis of the gut mycobiota showed enrichment of Saccharomycetes in IBS. Culturomics analysis of fungal isolates from feces showed enrichment of Candida spp. displaying from IBS a clonal expansion and a distinct genotypic profiles and different phenotypical features when compared to HS of Candida albicans isolates. Alongside the well-characterized gut bacterial dysbiosis in IBS, this study shed light on a yet poorly explored fungal component of the intestinal ecosystem, the gut mycobiota. Our results showed a differential fungal community in IBS compared to HS, suggesting potential for new insights on the involvement of the gut mycobiota in IBS. KEY POINTS: Comparison of gut microbiota and mycobiota between IBS and healthy subjects Investigation of cultivable fungi in IBS and healthy subjects Candida albicans isolates result more virulent in IBS subjects compared to healthy subjects

Effect of bioactive compounds released from Brassicaceae defatted seed meals on bacterial load in pig manure.

Animal manure application to soils is considered to be one of the main cause of antibiotic and bacterial pathogen spread in the environment. Pig livestock, which is the source of one of the most used fertilizer for cultivated land, is also a hotspot for antibiotics and antibiotic-resistant bacteria. Besides harsh chemical and physical sanitization treatments for the abatement of antibiotics and bacterial load in livestock waste, more sustainable and environmentally friendly strategies need to be considered. In this context, the use of natural substances which are proved useful for pest and disease control is currently under exploration for their role in the reduction of bacterial pathogen population. Among these, plants and derived products from the Brassicaceae family, characterized by the presence of a defensive glucosinolate-myrosinase enzymatic system, have been successfully exploited for years in agriculture using the so-called biofumigation technique against crop diseases. Although the application of biofumigation to suppress a range of soil borne pests has been well documented, no studies have been examined to reduce bacterial population in animal waste. In the present study, the release and the antibacterial activity of bioactive compounds deriving from different Brassicaceae defatted seed meals against pathogens and bacterial population in pig manure is addressed. Rapistrum rugosum and Brassica nigra defatted seed meals were found to be the most active products against tested pathogens and able to significantly reduce the bacterial load in the manure

A pilot study of the role of corn dextrin and milk peptides supplementation on faecal microbiota in healthy adults

The gastrointestinal microbiota has an important role in human health. Dietary interventions are of great interest to modulate the composition and metabolic functions of the gut microbial communities and to improve health, and prevent or treat diseases. Consumption of prebiotics is one dietary strategy for beneficial manipulation of the gut microbiota, because it allows increasing the fibre intake, especially in people with western dietary habits, who do not take the recommended daily amount of fiber. Interestingly, milk peptides can also positively affect the beneficial gut microorganisms. The present work is a pilot study aimed to investigate the effect of a prebiotic supplementation on composition and metabolic activity of microorganisms living in the human gut. In this trial, 12 healthy subjects received 10g/die of supplement Biotransit\uae, composed by corn derived dextrin and milk peptides, produced and marketed in Italy by Depofarma (Italy), for 4 weeks with a 2 weeks washout. Outcome measures were assessed at four time points (before the supplementation T0-1, T0-2, at the end of intervention, T30 and after washout, T45), including gut microbiota profiling by 16S rRNA gene sequencing and intestinal functional metabolism measuring faecal Short Chain Fatty Acid concentrations (SCFAs). The effects of the Biotransit supplementation on bifidobacteria were also assessed with culture dependent techniques. Gut microbiota analysis revealed that Biotransit\uae supplementation after 30 days did not exert effects on the overall gut microbiota structure. Although no significant differences on alpha diversity were obtained, we observed an increase of diversity after 30 days of treatment. Beta diversity analysis, calculated on Bray-Curtis distances revealed significant differences comparing T0 vs T45 and T30 vs T45. Interestingly, at T45, we found an enrichment of Porphyromonadaceae. Biotransit\uae induced quantitative changes in cultivable bifidobacteria with increased amount at T45, even if the total number of species has not been influenced. Biotransit\uae supplementation is also associated to an increase total SCFAs concentration in T30 and T45, in particular related to acetate, propionate and butyrate (p < 0.05). Future study will be aimed to follow the time course of the persistence of this effect after the end of treatment

Short- and long-term effects of essential oils on swine spermatozoa during liquid phase refrigeration

: The application of essential oils as potential alternatives to antibiotics in swine semen storage is promising, due to their antioxidant and antibacterial properties. However, detrimental effects on spermatozoa should be clarified first. The aim of this study was to evaluate 9 essential oils (EOs; Satureja montana, Pelargonium graveolens, Cymbopogon nardus, Melaleuca leucadendron, Eucaliptus globulus, Citrus limon, Lavandula angustifolia, Lavandula hybrida, Mentha piperita) and a blend (GL mix) on key morpho-functional parameters of swine spermatozoa. Test compounds were firstly chemo-characterized and experimental doses were prepared by suspending a fixed number of spermatozoa with 3 different concentrations (0.1, 0.5, 1 mg/mL) of EOs. Experimental doses were stored at 16 °C and sampled after 3 and 120 h for analysis. Overall, S. montana, P. graveolens and L. angustifolia EOs induced the strongest alterations, with C. nardus and E. globulus EOs being the best tolerated. Swine spermatozoa represent a good preliminary testing platform to screen toxicity and its different patterns. The comprehensive overview on the potential mechanisms of action of some of the most common EOs, despite of the direct aim of the study being swine reproduction, may be exploited in other fields of research within both veterinary and human medicine