Is Pseudobutyrivibrio xylanivorans strain Mz5T suitable as a probiotic? An in vitro study

The structure and functional profile of ruminal microbiota in young and adult reindeers (Rangifer tarandus) consuming natural winter-spring and summer-autumn seasonal diets

Background

The key natural area of Russian reindeer (Rangifer tarandus, Nenets breed) is arctic zones, with severe climatic conditions and scarce feed resources, especially in the cold winter season. The adaptation of reindeer to these conditions is associated not only with the genetic potential of the animal itself. The rumen microbiome provides significant assistance in adapting animals to difficult conditions by participating in the fiber digestion. The aim of our study is to investigate the taxonomy and predicted metabolic pathways of the ruminal microbiota (RM) during the winter–spring (WS) and summer–autumn (SA) seasons, in calves and adult reindeer inhabiting the natural pastures of the Yamalo-Nenetsky Autonomous District of the Russian Federation.

Methods

The RM in reindeer was studied using the Next Generation Sequencing method with the MiSeq (Illumina, San Diego, CA, USA) platform. Reconstruction and prediction of functional profiles of the metagenome, gene families, and enzymes were performed using the software package PICRUSt2 (v.2.3.0).

Results

The nutritional value of WS and SA diets significantly differed. Crude fiber content in the WS diet was higher by 22.4% (p < 0.05), compared to SA, indicating possibly poorer digestibility and necessity of the adaptation of the RM to this seasonal change. A total of 22 bacterial superphyla and phyla were found in the rumen, superphylum Bacteroidota and phylum Firmicutes being the dominating taxa (up to 48.1% ± 4.30% and 46.1% ± 4.80%, respectively); while only two archaeal phyla presented as minor communities (no more then 0.54% ± 0.14% totally). The percentages of the dominating taxa were not affected by age or season. However, significant changes in certain minor communities were found, with seasonal changes being more significant than age-related ones. The percentage of phylum Actinobacteriota significantly increased (19.3-fold) in SA, compared to WS (p = 0.02) in adults, and the percentage of phylum Cyanobacteria increased up to seven-fold (p = 0.002) in adults and calves. Seasonal changes in RM can improve the ability of reindeer to withstand the seasons characterized by a low availability of nutrients. The PICRUSt2 results revealed 257 predicted metabolic pathways in RM: 41 pathways were significantly (p < 0.05) influenced by season and/or age, including the processes of synthesis of vitamins, volatile fatty acids, and pigments; metabolism of protein, lipids, and energy; pathogenesis, methanogenesis, butanediol to pyruvate biosynthesis, cell wall biosynthesis, degradation of neurotransmitters, lactic acid fermentation, and biosynthesis of nucleic acids. A large part of these changeable pathways (13 of 41) was related to the synthesis of vitamin K homologues.

Conclusion

The results obtained improve our knowledge on the structure and possible metabolic pathways of the RM in reindeer, in relation to seasonal changes.

Probiotic biomarkers and models upside down: From humans to animals

Probiotics development for animal farming implies thorough testing of a vast variety of properties, including adhesion, toxicity, host cells signaling modulation, and immune effects. Being diverse, these properties are often tested individually and using separate biological models, with great emphasis on the host organism. Although being precise, this approach is cost-ineffective, limits the probiotics screening throughput and lacks informativeness due to the 'one model - one test - one property' principle. There is а solution coming from human-derived cells and in vitro systems, an extraordinary example of human models serving animal research. In the present review, we focus on the current outlooks of employing human-derived in vitro biological models in probiotics development for animal applications, examples of such studies and the analysis of concordance between these models and host-derived in vivo data. In our opinion, human-cells derived screening systems allow to test several probiotic properties at once with reasonable precision, great informativeness and less expenses and labor effort.

Effects of Maresin 1 (MaR1) on Colonic Inflammation and Gut Dysbiosis in Diet-Induced Obese Mice

The aim of this study was to characterize the effects of Maresin 1 (MaR1), a DHA-derived pro-resolving lipid mediator, on obesity-related colonic inflammation and gut dysbiosis in diet-induced obese (DIO) mice. In colonic mucosa of DIO mice, the MaR1 treatment decreased the expression of inflammatory genes, such as Tnf-α and Il-1β. As expected, the DIO mice exhibited significant changes in gut microbiota composition at the phylum, genus, and species levels, with a trend to a higher Firmicutes/Bacteroidetes ratio. Deferribacteres and Synergistetes also increased in the DIO animals. In contrast, these animals exhibited a significant decrease in the content of Cyanobacteria and Actinobacteria. Treatment with MaR1 was not able to reverse the dysbiosis caused by obesity on the most abundant phyla. However, the MaR1 treatment increased the content of P. xylanivorans, which have been considered to be a promising probiotic with healthy effects on gut inflammation. Finally, a positive association was found between the Deferribacteres and Il-1β expression, suggesting that the increase in Deferribacteres observed in obesity could contribute to the overexpression of inflammatory cytokines in the colonic mucosa. In conclusion, MaR1 administration ameliorates the inflammatory state in the colonic mucosa and partially compensates changes on gut microbiota caused by obesity.

Pseudobutyrivibrio xylanivorans adhesion to epithelial cells

The ruminal bacteria Pseudobutyrivibrio xylanivorans strain 2 (P. xylanivorans 2), that mediates the digestion of plant fiber, is considered an attractive candidate for probiotics. Adherence to the epithelium of the digestive tract of the host is one of the major requirements for probiotics. In this study, we assessed the adhesion of P. xylanivorans 2 to SW480 cells and characterized this process utilizing multiple microscopy approaches. Our results indicate that a multiplicity of infection of 200 CFU/cell allows the highest bacteria to cell binding ratio, with a lower percentage of auto-agglutination events. The comparison of the adherence capacity subjected heat-shock treatment (100 °C, 1 min), which produces the denaturalization of proteins at the bacterial surface, as opposed untreated P. xylanivorans, suggested that this bacteria may attach to SW480 cells utilizing a proteinaceous structure. Confocal microscopy analyses indicate that P. xylanivorans 2 attachment induces the formation of F-actin-enriched areas on the surface of SW480 cells. Transmission electron microscopy (TEM) revealed the formation of a structure similar to a pedestal in the area of the epithelial cell surface, where the bacterium rests. Finally, a casual finding of TEM analysis of transverse and longitudinal thin-sections of P. xylanivorans 2, revealed irregular intra-cytoplasmic structures compatibles with the so-called bacterial microcompartments. This is the first ultrastructural description of bacterial microcompartments-like structures in the genus Pseudobutyrivibrio.

Biogas production from brewery spent grain enhanced by bioaugmentation with hydrolytic anaerobic bacteria

Lignocellulosic substrates are widely available but not easily applied in biogas production due to their poor anaerobic degradation. The effect of bioaugmentation by anaerobic hydrolytic bacteria on biogas production was determined by the biochemical methane potential assay. Microbial biomass from full scale upflow anaerobic sludge blanket reactor treating brewery wastewater was a source of active microorganisms and brewery spent grain a model lignocellulosic substrate. Ruminococcus flavefaciens 007C, Pseudobutyrivibrio xylanivorans Mz5(T), Fibrobacter succinogenes S85 and Clostridium cellulovorans as pure and mixed cultures were used to enhance the lignocellulose degradation and elevate the biogas production. P. xylanivorans Mz5(T) was the most successful in elevating methane production (+17.8%), followed by the coculture of P. xylanivorans Mz5(T) and F. succinogenes S85 (+6.9%) and the coculture of C. cellulovorans and F. succinogenes S85 (+4.9%). Changes in microbial community structure were detected by fingerprinting techniques.

Isolation of Pseudobutyrivibrio ruminis and Pseudobutyrivibrio xylanivorans from rumen of Creole goats fed native forage diet

We isolated and identified functional groups of bacteria in the rumen of Creole goats involved in ruminal fermentation of native forage shrubs. The functional bacterial groups were evaluated by comparing the total viable, total anaerobic, cellulolytic, hemicellulolytic, and amylolytic bacterial counts in the samples taken from fistulated goats fed native forage diet (Atriplex lampa and Prosopis flexuosa). Alfalfa hay and corn were used as control diet. The roll tubes method increased the possibility of isolating and 16S rDNA gene sequencing allowed definitive identification of bacterial species involved in the ruminal fermentation. The starch and fiber contents of the diets influenced the number of total anaerobic bacteria and fibrolytic and amylolytic functional groups. Pseudobutyrivibrio ruminis and Pseudobutyrivibrio xylanivorans were the main species isolated and identified. The identification of bacterial strains involved in the rumen fermentation helps to explain the ability of these animals to digest fiber plant cell wall contained in native forage species.

Review: The use of direct fed microbials to mitigate pathogens and enhance production in cattle

McAllister, T. A., Beauchemin, K. A., Alazzeh, A. Y., Baah, J., Teather, R. M. and Stanford, K. 2011. Review: The use of direct fed microbials to mitigate pathogens and enhance production in cattle. Can. J. Anim. Sci. 91: 193–211. Direct-fed microbials (DFM) have been employed in ruminant production for over 30 yr. Originally, DFM were used primarily in young ruminants to accelerate establishment of the intestinal microflora involved in feed digestion and to promote gut health. Further advancements led to more sophisticated mixtures of DFM that are targeted at improving fiber digestion and preventing ruminal acidosis in mature cattle. Through these outcomes on fiber digestion/rumen health, second-generation DFM have also resulted in improvements in milk yield, growth and feed efficiency of cattle, but results have been inconsistent. More recently, there has been an emphasis on the development of DFM that exhibit activity in cattle against potentially zoonotic pathogens such as Escherichia coli O157:H7, Salmonella spp. and Staphylococcus aureus. Regulatory requirements have limited the microbial species within DFM products to organisms that are generally recognized as safe, such as lactic acid-producing bacteria (e.g., Lactobacillus and Enterococcus spp.), fungi (e.g., Aspergillus oryzae), or yeast (e.g., Saccharomyces cerevisiae). Direct-fed microbials of rumen origin, involving lactate-utilizing species (e.g., Megasphaera elsdenii, Selenomonas ruminantium, Propionibacterium spp.) and plant cell wall-degrading isolates of Butyrivibrio fibrisolvens have also been explored, but have not been commercially used. Development of DFM that are efficacious over a wide range of ruminant production systems remains challenging because[0] comprehensive knowledge of microbial ecology is lacking. Few studies have employed molecular techniques to study in detail the interaction of DFM with native microbial communities or the ruminant host. Advancements in the metagenomics of microbial communities and the genomics of microbial–host interactions may enable DFM to be formulated to improve production and promote health, responses that are presently often achieved through the use of antimicrobials in cattle.

Culture-independent identification of gut bacteria correlated with the onset of diabetes in a rat model

Bacteria associated with the onset of type 1 diabetes in a rat model system were identified. In two experiments, stool samples were collected at three time points after birth from bio-breeding diabetes-prone (BB-DP) and bio-breeding diabetes-resistant (BB-DR) rats. DNA was isolated from these samples and the 16S rRNA gene was amplified using universal primer sets. In the first experiment, bands specific to BB-DP and BB-DR genotypes were identified by automated ribosomal intergenic spacer analysis at the time of diabetes onset in BB-DP. Lactobacillus and Bacteroides strains were identified in the BB-DR- and BB-DP-specific bands, respectively. Sanger sequencing showed that the BB-DP and BB-DR bacterial communities differed significantly but too few reads were available to identify significant differences at the genus or species levels. A second experiment confirmed these results using higher throughput pyrosequencing and quantitative PCR of 16S rRNA with more rats per genotype. An average of 4541 and 3381 16S rRNA bacterial reads were obtained from each of the 10 BB-DR and 10 BB-DP samples collected at time of diabetes onset. Nine genera were more abundant in BB-DP whereas another nine genera were more abundant in BB-DR. Thirteen and eleven species were more abundant in BB-DP and BB-DR, respectively. An average of 23% and 10% of all reads could be classified at the genus and species levels, respectively. Quantitative PCR verified the higher abundance of Lactobacillus and Bifidobacterium in the BB-DR samples. Whether these changes are caused by diabetes or are involved in the development of the disease is unknown.

Adaptation of adhesion test using Caco-2 cells for anaerobic bacterium Pseudobutyrivibrio xylanivorans, a probiotic candidate

Pseudobutyrivibrio xylanivorans strain Mz5(T), an anaerobic bacterium (originating from the rumen of a Holstein-Friesian cow), has some attributes that make it a possible probiotic strain (very active hydrolases, bacteriocin and conjugated linoleic acid production). For the estimation of its adhesion ability, the adhesion test on Caco-2 cells was introduced and adapted. The adhesion was performed in an anaerobic glove box in standard 24-well plates at neutral pH for 30 min. The best method for separation of the adhered bacteria from Caco-2 cells appeared to be homogenization with an automatic pipette. The number of adhered bacteria was too small to be determined microscopically, so a new approach, i.e. detection of the apparent lag phase in liquid growth medium was tested. Under the selected assay conditions 1.04 bacterial cells from the late exponential phase adhered to one Caco-2 cell, which confirms the adhesion capability of P. xylanivorans Mz5(T). The adapted adhesion test using Caco-2 cells is suitable for estimation of adhesion capability of anaerobic bacteria.

Diet-dependent shifts in ruminal butyrate-producing bacteria

The influence of a host's diet on Butyrivibrio and Pseudobutyrivibrio populations was investigated by competitive PCR. Specific primers were designed and competitive PCRs developed for both groups. Results (from 4 cows with different diets) suggested that high-fiber intake essentially increases the Butyrivibrio amounts in the rumen, whereas high-energy food additives lead to its suppression. The Pseudobutyrivibrio concentration also changed during the experiment but without any significant relation to the host's diet.

Purification and characterization of xylanases from Aspergillus giganteus

A strain of Aspergillus giganteus cultivated in a medium with xylan produced two xylanases (xylanase I and II) which were purified to homogeneity. Their molar mass, estimated by SDS-PAGE, were 21 and 24 kDa, respectively. Both enzymes are glycoproteins with 50 degrees C temperature optimum; optimum pH was 6.0-6.5 for xylanase I and 6.0 for xylanase II. At 50 degrees C xylanase I exhibited higher thermostability than xylanase II. Hg2+, Cu2+ and SDS were strong inhibitors, 1,4-dithiothreitol stimulated the reaction of both enzymes. Both xylanases are xylan-specific; kinetic parameters indicated higher efficiency in the hydrolysis of oat spelts xylan. In hydrolysis of this substrate, xylotriose, xylotetraose and larger xylooligosaccharides were released and hence the enzymes were classified as endoxylanases.