Isolation and characterization of a bacteriocin (Butyrivibriocin AR10) from the ruminal anaerobe Butyrivibrio fibrisolvens AR10: evidence in support of the widespread occurrence of bacteriocin-like activity among ruminal isolates of B. fibrisolvens

Bacteriocins: Curial guardians of gastrointestinal tract

The human gastrointestinal (GI) tract microbiome secretes various metabolites that play pivotal roles in maintaining host physiological balance and influencing disease progression. Among these metabolites, bacteriocins-small, heat-stable peptides synthesized by ribosomes-are notably prevalent in the GI region. Their multifaceted benefits have garnered significant interest in the scientific community. This review comprehensively explores the methods for mining bacteriocins (traditional separation and purification, bioinformatics, and artificial intelligence), their effects on the stomach and intestines, and their complex bioactive mechanisms. These mechanisms include flora regulation, biological barrier restoration, and intervention in epithelial cell pathways. By detailing each well-documented bacteriocin, we reveal the diverse ways in which bacteriocins interact with the GI environment. Moreover, the future research direction is prospected. By further studying the function and interaction of intestinal bacteriocins, we can discover new pharmacological targets and develop drugs targeting intestinal bacteriocins to regulate and improve human health. It provides innovative ideas and infinite possibilities for further exploration, development, and utilization of bacteriocins. The inevitable fact is that the continuously exploration of bacteriocins is sure to bring the promising future for demic GI health understanding and interference strategy.

Increased Proportion of Fiber-Degrading Microbes and Enhanced Cecum Development Jointly Promote Host To Digest Appropriate High-Fiber Diets

Previous study found that appropriate high-fiber diet (containing 19.10% total dietary fiber [TDF], treatment II) did not reduce apparent fiber digestibility of Chinese Suhuai finishing pigs and increased the yield of short-chain fatty acids (SCFAs), but too high-fiber diet (containing 24.11% TDF, treatment IV) significantly reduced apparent fiber digestibility compared with normal diet (containing 16.70% TDF, control group). However, characteristics of microbiota at the species level and histological structure in pigs with the ability to digest appropriate high-fiber diets were still unknown. This study conducted comparative analysis of cecal physiology and microbial populations colonizing cecal mucosa. The results showed intestinal development indexes including cecum length, densities of cecal goblet cells, and renewal of cecal epithelial cells in treatment II and IV had better performance than those in the control. Paludibacter jiangxiensis, Coprobacter fastidiosus, Bacteroides coprocola CAG:162, Bacteroides barnesiae, and Parabacteroides merdae enriched in treatment II expressed large number of glycoside hydrolase (GH)-encoding genes and had the largest number of GH families. In addition, pathogenic bacteria (Shigella sonnei, Mannheimia haemolytica, and Helicobacter felis) were enriched in treatment IV. Correlation analysis revealed that the intestinal development index positively correlated with the relative abundance of cecal mucosal microbiota and the amount of digested fiber. These results indicated that increased proportions of fiber-degrading microbes and enhanced intestinal development jointly promote the host to digest an appropriate high-fiber diet. However, although too-high fiber levels in diet could maintain the adaptive development of cecal epithelium, the proportions of pathogenic bacteria increased, which might lead to a decrease of fiber digestion in pigs. IMPORTANCE Although studies about the effects of dietary fiber on fiber digestion and intestinal microbiota of pigs were widely in progress, few studies have been conducted on the dynamic response of intestinal microbiota to dietary fiber levels, and the characteristics of intestinal microbiota and intestinal epithelial development adapted to high-fiber diet s were still unclear. Appropriate high fiber promoted the thickness of large intestine wall, increased the density of cecal goblet cells, and promoted the renewal of cecal epithelial cells. In addition, appropriate high fiber improves the microbial abundance with fiber-digesting potential. However, excessive dietary fiber caused an increase in the abundance of pathogenic bacteria. These results indicated that an increased proportion of fiber-degrading microbes and enhanced intestinal development jointly promote host to digest appropriate high-fiber diets. However, although too-high fiber levels in diet could maintain the adaptive development of cecal epithelium, the proportions of pathogenic bacteria increased, which might lead to a decrease of fiber digestion in pigs. Our data provided a theoretical basis for rational and efficient utilization of unconventional feed resources in pig production.

Degradation of Cellulose and Hemicellulose by Ruminal Microorganisms

As major structural components of plant cell walls, cellulose and hemicellulose are degraded and fermented by anaerobic microbes in the rumen to produce volatile fatty acids, the main nutrient source for the host. Cellulose degradation is carried out primarily by specialist bacteria, with additional contributions from protists and fungi, via a variety of mechanisms. Hemicelluloses are hydrolyzed by cellulolytic bacteria and by generalist, non-cellulolytic microbes, largely via extracellular enzymes. Cellulose hydrolysis follows first-order kinetics and its rate is limited by available substrate surface area. Nevertheless, its rate is at least an order of magnitude more rapid than in anaerobic digesters, due to near-obligatory adherence of microbial cells to the cellulose surface, and a lack of downstream inhibitory effects; in the host animal, fiber degradation rate is also enhanced by the unique process of rumination. Cellulolytic and hemicellulolytic microbes exhibit intense competition and amensalism, but they also display mutualistic interactions with microbes at other trophic levels. Collectively, the fiber-degrading community of the rumen displays functional redundancy, partial niche overlap, and convergence of catabolic pathways that all contribute to stability of the ruminal fermentation. The superior hydrolytic and fermentative capabilities of ruminal fiber degraders make them promising candidates for several fermentation technologies.

Mechanism of Action of Ribosomally Synthesized and Post-Translationally Modified Peptides

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a natural product class that has undergone significant expansion due to the rapid growth in genome sequencing data and recognition that they are made by biosynthetic pathways that share many characteristic features. Their mode of actions cover a wide range of biological processes and include binding to membranes, receptors, enzymes, lipids, RNA, and metals as well as use as cofactors and signaling molecules. This review covers the currently known modes of action (MOA) of RiPPs. In turn, the mechanisms by which these molecules interact with their natural targets provide a rich set of molecular paradigms that can be used for the design or evolution of new or improved activities given the relative ease of engineering RiPPs. In this review, coverage is limited to RiPPs originating from bacteria.

Functional and phylogenetic analyses of camel rumen microbiota associated with different lignocellulosic substrates

Rumen microbiota facilitates nutrition through digestion of recalcitrant lignocellulosic substrates into energy-accessible nutrients and essential metabolites. Despite the high similarity in rumen microbiome structure, there might be distinct functional capabilities that enable different ruminant species to thrive on various lignocellulosic substrates as feed. Here, we applied genome-centric metagenomics to explore phylogenetic diversity, lignocellulose-degrading potential and fermentation metabolism of biofilm-forming microbiota colonizing 11 different plant substrates in the camel rumen. Diversity analysis revealed significant variations in the community of rumen microbiota colonizing different substrates in accordance with their varied physicochemical properties. Metagenome reconstruction recovered genome sequences of 590 bacterial isolates and one archaeal lineage belonging to 20 microbial phyla. A comparison to publicly available reference genomes and rumen metagenome-assembled genomes revealed that most isolates belonged to new species with no well-characterized representatives. We found that certain low abundant taxa, including members of Verrucomicrobiota, Planctomycetota and Fibrobacterota, possessed a disproportionately large number of carbohydrate active enzymes per Mb of genome, implying their high metabolic potential to contribute to the rumen function. In conclusion, we provided a detailed picture of the diversity and functional significance of rumen microbiota colonizing feeds of varying lignocellulose composition in the camel rumen. A detailed analysis of 591 metagenome-assembled genomes revealed a network of interconnected microbiota and highlighted the key roles of certain taxonomic clades in rumen function, including those with minimal genomes (e.g., Patescibacteria). The existence of a diverse array of gene clusters encoding for secondary metabolites unveiled the specific functions of these biomolecules in shaping community structure of rumen microbiota.

Gut Microbiota and Their Role in Health and Metabolic Disease of Dairy Cow

Ruminants are mostly herbivorous animals that employ rumen fermentation for the digestion of feed materials, including dairy cows. Ruminants consume plant fibre as their regular diet, but lack the machinery for their digestion. For this reason, ruminants maintain a symbiotic relation with microorganisms that are capable of producing enzymes to degrade plant polymers. Various species of microflora including bacteria, protozoa, fungi, archaea, and bacteriophages are hosted at distinct concentrations for accomplishing complete digestion. The ingested feed is digested at a defined stratum. The polysaccharic plant fibrils are degraded by cellulolytic bacteria, and the substrate formed is acted upon by other bacteria. This sequential degradative mechanism forms the base of complete digestion as well as harvesting energy from the ingested feed. The composition of microbiota readily gets tuned to the changes in the feed habits of the dairy cow. The overall energy production as well as digestion is decided by the intactness of the resident communal flora. Disturbances in the homogeneity gastrointestinal microflora has severe effects on the digestive system and various other organs. This disharmony in communal relationship also causes various metabolic disorders. The dominance of methanogens sometimes lead to bloating, and high sugar feed culminates in ruminal acidosis. Likewise, disruptive microfloral constitution also ignites reticuloperitonitis, ulcers, diarrhoea, etc. The role of symbiotic microflora in the occurrence and progress of a few important metabolic diseases are discussed in this review. Future studies in multiomics provides platform to determine the physiological and phenotypical upgradation of dairy cow for milk production.

Compositional and Functional Characteristics of Swine Slurry Microbes through 16S rRNA Metagenomic Sequencing Approach

Traditionally slurry is used as source of nitrogen, phosphorous, and potassium in bio fertilizers to improve crop production. However, poorly managed slurry causes a hazardous effect to the environment by producing greenhouse gases, causing the eutrophication of water bodies, and polluting the groundwater. It has been largely reported that the microbial presence in slurry causing a diverse effect on its storage and disposal system. However, the diversity of bacterial populations in pig slurries remains largely unexplored. Here we report the bacterial diversity present in the slurry from slurry pits, and the effect of storage time on bacterial population. We collected 42 samples from three different pig slurry pits, as three replicates from each one until the 14th week. We used the 16S rRNA, Quantitative Insights Into Microbial Ecology (QIIME) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) protocols for the metagenomic downstream analysis. Taxonomic annotation using the Greengenes metagenomic database indicated that on an average 76.2% Firmicutes, 14.4% Bacteroidetes, 4.9% Proteobacteria, etc. microbial populations were present. Comparative microbial analysis showed that the population of Firmicutes decreased from the first to the 14th week, whereas the population of Bacteroidetes increased from the first to the 14th week. Through principal coordinate analysis (PCoA), (linear discriminant analysis effect size (LEfSe), and Pearson's correlation analysis, we found microbial biomarkers according to the storage time point. All bacterial populations were well clustered according to the early, middle, and last weeks of storage. LEfSe showed that Actinobacteria, Lachnospiraceae, Ruminococcaceae, and Bacteroidia are dominantly present in first, seventh, ninth, and 14th week, respectively. Lachnospiraceae and Ruminococcaceae are ubiquitous gastrointestinal non-pathogenic bacteria. KEGG pathways, such as membrane transport, carbohydrate and amino acid metabolism, genetic replication and repair, were significant among all samples. Such a KEGG pathway may indicate the association between the host organism's metabolic activity and the microbes present in the gastro intestinal tract (GIT).

Adding Appropriate Fiber in Diet Increases Diversity and Metabolic Capacity of Distal Gut Microbiota Without Altering Fiber Digestibility and Growth Rate of Finishing Pig

The digestion ability of pigs to dietary fiber is derived from their intestinal microbiota, especially hindgut microbiota. However, tolerance of pigs to high dietary fiber and the changes of microbiota profile with fiber levels are still unclear. To investigate the changes of gut microbiota with dietary fiber and its relationship with fiber digestibility, we conducted comparative analyses of growth rate, apparent fiber digestibility, gut microbiota and volatile fatty acid (VFA) profiles in Chinese Suhuai pigs feeding diets with different defatted rice bran (DFRB) fiber levels. We found that dietary fiber level had no effect on the growth rate of Suhuai pigs. Although the apparent digestibility of Cellulose, insoluble dietary fiber (IDF) and total dietary fiber (TDF) decreased with dietary fiber level, we found that the apparent digestibility of Cellulose, IDF and TDF of Suhuai pigs was not changed when provided with diet containing 19.10% TDF (as feed basis). The pigs provided with diet containing 19.10% TDF had higher microbial richness, proportions of several fiber-degrading bacteria taxa at genus level and predicted microbial functions (such as carbohydrate metabolism, energy metabolism) in cecum compared to those fed with basal diet. In addition, the fiber-induced increasing of fiber-degrading bacteria promoted the VFAs metabolism, which potentially helped Suhuai pigs to maintain growth rate. However, as TDF reached to 24.11% (as feed basis), the apparent digestibility of fiber decreased and the positive effect on intestine microbiota in caecum were absent. Together, our data suggest that appropriate fiber level could increase the diversity and metabolic capacity of distal gut microbiota to improve the utilization efficiency of fiber resources without altering the growth rate of pigs.

Bioinformatic prospecting and phylogenetic analysis reveals 94 undescribed circular bacteriocins and key motifs

Background

Circular bacteriocins are antimicrobial peptides produced by bacteria with a N and C termini ligation. They have desirable properties such as activity at low concentrations along with thermal, pH and proteolytic resistance. There are twenty experimentally confirmed circular bacteriocins as part of bacteriocin gene clusters, with transport, membrane and immunity proteins. Traditionally, novel antimicrobials are found by testing large numbers of isolates against indicator strains, with no promise of corresponding novel sequence.

Results

Through bioprospecting publicly available sequence databases, we identified ninety-nine circular bacteriocins across a variety of bacteria bringing the total to 119. They were grouped into two families within class I modified bacteriocins (i and ii) and further divided into subfamilies based on similarity to experimentally confirmed circular bacteriocins. Within subfamilies, sequences overwhelmingly shared similar characteristics such as sequence length, presence of a polybasic region, conserved locations of aromatic residues, C and N termini, gene clusters similarity, translational coupling and hydrophobicity profiles. At least ninety were predicted to be putatively functional based on gene clusters. Furthermore, bacteriocins identified from Enterococcus, Staphylococcus and Streptococcus species may have activity against clinically relevant strains, due to the presence of putative immunity genes required for expression in a toxin-antitoxin system. Some strains such as Paenibacillus larvae subsp. pulvifaciens SAG 10367 contained multiple circular bacteriocin gene clusters from different subfamilies, while some strains such as Bacillus cereus BCE-01 contained clusters with multiple circular bacteriocin structural genes.

Conclusions

Sequence analysis provided rapid insight into identification of novel, putative circular bacteriocins, as well as conserved genes likely essential for circularisation. This represents an expanded library of putative antimicrobial proteins which are potentially active against human, plant and animal pathogens.

Comparative Genomics of Rumen Butyrivibrio spp. Uncovers a Continuum of Polysaccharide-Degrading Capabilities

Feeding a global population of 8 billion people and climate change are the primary challenges facing agriculture today. Ruminant livestock are important food-producing animals, and maximizing their productivity requires an understanding of their digestive systems and the roles played by rumen microbes in plant polysaccharide degradation. Members of the genera Butyrivibrio and Pseudobutyrivibrio are a phylogenetically diverse group of bacteria and are commonly found in the rumen, where they are a substantial source of polysaccharide-degrading enzymes for the depolymerization of lignocellulosic material. Our findings have highlighted the immense enzymatic machinery of Butyrivibrio and Pseudobutyrivibrio species for the degradation of plant fiber, suggesting that these bacteria occupy similar niches but apply different degradation strategies in order to coexist in the competitive rumen environment.

Plant polysaccharide breakdown by microbes in the rumen is fundamental to digestion in ruminant livestock. Bacterial species belonging to the rumen genera Butyrivibrio and Pseudobutyrivibrio are important degraders and utilizers of lignocellulosic plant material. These bacteria degrade polysaccharides and ferment the released monosaccharides to yield short-chain fatty acids that are used by the ruminant for growth and the production of meat, milk, and fiber products. Although rumen Butyrivibrio and Pseudobutyrivibrio species are regarded as common rumen inhabitants, their polysaccharide-degrading and carbohydrate-utilizing enzymes are not well understood. In this study, we analyzed the genomes of 40 Butyrivibrio and 6 Pseudobutyrivibrio strains isolated from the plant-adherent fraction of New Zealand dairy cows to explore the polysaccharide-degrading potential of these important rumen bacteria. Comparative genome analyses combined with phylogenetic analysis of their 16S rRNA genes and short-chain fatty acid production patterns provide insight into the genomic diversity and physiology of these bacteria and divide Butyrivibrio into 3 species clusters. Rumen Butyrivibrio bacteria were found to encode a large and diverse spectrum of degradative carbohydrate-active enzymes (CAZymes) and binding proteins. In total, 4,421 glycoside hydrolases (GHs), 1,283 carbohydrate esterases (CEs), 110 polysaccharide lyases (PLs), 3,605 glycosyltransferases (GTs), and 1,706 carbohydrate-binding protein modules (CBM) with predicted activities involved in the depolymerization and transport of the insoluble plant polysaccharides were identified. Butyrivibrio genomes had similar patterns of CAZyme families but varied greatly in the number of genes within each category in the Carbohydrate-Active Enzymes database (CAZy), suggesting some level of functional redundancy. These results suggest that rumen Butyrivibrio species occupy similar niches but apply different degradation strategies to be able to coexist in the rumen.

IMPORTANCE Feeding a global population of 8 billion people and climate change are the primary challenges facing agriculture today. Ruminant livestock are important food-producing animals, and maximizing their productivity requires an understanding of their digestive systems and the roles played by rumen microbes in plant polysaccharide degradation. Members of the genera Butyrivibrio and Pseudobutyrivibrio are a phylogenetically diverse group of bacteria and are commonly found in the rumen, where they are a substantial source of polysaccharide-degrading enzymes for the depolymerization of lignocellulosic material. Our findings have highlighted the immense enzymatic machinery of Butyrivibrio and Pseudobutyrivibrio species for the degradation of plant fiber, suggesting that these bacteria occupy similar niches but apply different degradation strategies in order to coexist in the competitive rumen environment.

Islands in the stream: from individual to communal fiber degradation in the rumen ecosystem

The herbivore rumen ecosystem constitutes an extremely efficient degradation machinery for the intricate chemical structure of fiber biomass, thus, enabling the hosting animal to digest its feed. The challenging task of deconstructing and metabolizing fiber is performed by microorganisms inhabiting the rumen. Since most of the ingested feed is comprised of plant fiber, these fiber-degrading microorganisms are of cardinal importance to the ecology of the rumen microbial community and to the hosting animal, and have a great impact on our environment and food sustainability. We summarize herein the enzymological fundamentals of fiber degradation, how the genes encoding these enzymes are spread across fiber-degrading microbes, and these microbes' interactions with other members of the rumen microbial community and potential effect on community structure. An understanding of these concepts has applied value for agriculture and our environment, and will also contribute to a better understanding of microbial ecology and evolution in anaerobic ecosystems.

Effects and immune responses of probiotic treatment in ruminants

Gut microbial colonization and establishment are vital to ruminant health and production. This review article focuses on current knowledge and methods used to understand and manipulate the gut microbial community in ruminant animals, with a special focus on probiotics treatment. This review highlights the most promising of studies in this area, including gut microbial colonization and establishment, effect of gastrointestinal tract microbial community on host mucosal innate immune function, impact of feeding strategies on gut microbial community, current probiotic treatments in ruminants, methods to manipulate the gut microbiota and associated antimicrobial compounds, and models and cell lines used in understanding the host immune response to probiotic treatments. As a lot of work in this area was done in humans and mice, this review article also includes up-to-date knowledge from relevant studies in human and mouse models. This review is a useful resource for scientists working in the areas of ruminant nutrition and health, and to researchers investigating the microbial ecology and its relation to animal health.

Gut microbes as future therapeutics in treating inflammatory and infectious diseases: Lessons from recent findings

The human gut microbiota has been the interest of extensive research in recent years and our knowledge on using the potential capacity of these microbes are growing rapidly. Microorganisms colonized throughout the gastrointestinal tract of human are coevolved through symbiotic relationship and can influence physiology, metabolism, nutrition and immune functions of an individual. The gut microbes are directly involved in conferring protection against pathogen colonization by inducing direct killing, competing with nutrients and enhancing the response of the gut-associated immune repertoire. Damage in the microbiome (dysbiosis) is linked with several life-threatening outcomes viz. inflammatory bowel disease, cancer, obesity, allergy, and auto-immune disorders. Therefore, the manipulation of human gut microbiota came out as a potential choice for therapeutic intervention of the several human diseases. Herein, we review significant studies emphasizing the influence of the gut microbiota on the regulation of host responses in combating infectious and inflammatory diseases alongside describing the promises of gut microbes as future therapeutics.

Antibiotics and specialized metabolites from the human microbiota

Human microbiota associated with each body site produce specialized molecules to kill human pathogens. Advanced bioinformatics tools will help to discover unique microbiome chemistry.

Structural Characterization and Bioactivity Analysis of the Two-Component Lantibiotic Flv System from a Ruminant Bacterium

The discovery of new ribosomally synthesized and post-translationally modified peptide natural products (RiPPs) has greatly benefitted from the influx of genomic information. The lanthipeptides are a subset of this class of compounds. Adopting the genome-mining approach revealed a novel lanthipeptide gene cluster encoded in the genome of Ruminococcus flavefaciens FD-1, an anaerobic bacterium that is an important member of the rumen microbiota of livestock. The post-translationally modified peptides were produced via heterologous expression in Escherichia coli. Subsequent structural characterization and assessment of their bioactivity revealed features reminiscent of and distinct from previously reported lanthipeptides. The lanthipeptides of R. flavefaciens FD-1 represent a unique example within two-component lanthipeptides, consisting of a highly conserved α-peptide and a diverse set of eight β-peptides.

Distribution and Genetic Diversity of Bacteriocin Gene Clusters in Rumen Microbial Genomes

Some species of ruminal bacteria are known to produce antimicrobial peptides, but the screening procedures have mostly been based on in vitro assays using standardized methods. Recent sequencing efforts have made available the genome sequences of hundreds of ruminal microorganisms. In this work, we performed genome mining of the complete and partial genome sequences of 224 ruminal bacteria and 5 ruminal archaea to determine the distribution and diversity of bacteriocin gene clusters. A total of 46 bacteriocin gene clusters were identified in 33 strains of ruminal bacteria. Twenty gene clusters were related to lanthipeptide biosynthesis, while 11 gene clusters were associated with sactipeptide production, 7 gene clusters were associated with class II bacteriocin production, and 8 gene clusters were associated with class III bacteriocin production. The frequency of strains whose genomes encode putative antimicrobial peptide precursors was 14.4%. Clusters related to the production of sactipeptides were identified for the first time among ruminal bacteria. BLAST analysis indicated that the majority of the gene clusters (88%) encoding putative lanthipeptides contained all the essential genes required for lanthipeptide biosynthesis. Most strains of Streptococcus (66.6%) harbored complete lanthipeptide gene clusters, in addition to an open reading frame encoding a putative class II bacteriocin. Albusin B-like proteins were found in 100% of the Ruminococcus albus strains screened in this study. The in silico analysis provided evidence of novel biosynthetic gene clusters in bacterial species not previously related to bacteriocin production, suggesting that the rumen microbiota represents an underexplored source of antimicrobial peptides.

Circular bacteriocins: biosynthesis and mode of action

Circular bacteriocins are a group of N-to-C-terminally linked antimicrobial peptides, produced by Gram-positive bacteria of the phylum Firmicutes. Circular bacteriocins generally exhibit broad-spectrum antimicrobial activity, including against common food-borne pathogens, such as Clostridium and Listeria spp. These peptides are further known for their high pH and thermal stability, as well as for resistance to many proteolytic enzymes, properties which make this group of bacteriocins highly promising for potential industrial applications and their biosynthesis of particular interest as a possible model system for the synthesis of highly stable bioactive peptides. In this review, we summarize the current knowledge on this group of bacteriocins, with emphasis on the recent progress in understanding circular bacteriocin genetics, biosynthesis, and mode of action; in addition, we highlight the current challenges and future perspectives for the application of these peptides.

Discovering the bacterial circular proteins: bacteriocins, cyanobactins, and pilins

Over recent years, several examples of natural ribosomally synthesized circular proteins and peptides from diverse organisms have been described. They are a group of proteins for which the precursors must be post-translationally modified to join the N and C termini with a peptide bond. This feature appears to confer a range of potential advantages because these proteins show increased resistance to proteases and higher thermodynamic stability, both of which improve their biological activity. They are produced by prokaryotic and eukaryotic organisms and show diverse biological activities, related mostly to a self-defense or competition mechanism of the producer organisms, with the only exception being the circular pilins. This minireview highlights ribosomally synthesized circular proteins produced by members of the domain Bacteria: circular bacteriocins, cyanobactins, and circular pilins. We pay special attention to the genetic organization of the biosynthetic machinery of these molecules, the role of circularization, and the differences in the possible circularization mechanisms.

Production and characterization of a bacteriocin from ruminal bacterium Ruminococcus albus 7

The characteristics of a bacteriocin from Ruminococcus albus 7 and its potential as an antibiotic alternative were examined in this study. The addition of 3 µM 3-phenylpropanoic acid (PPA) and 0.2% Tween 80 to the culturing medium improved bacteriocin production by 2.5-fold. Native polyacrylamide gel electrophoresis of the antagonistically active gel filtration fraction established that the molecular weight of the R. albus 7 bacteriocin was approximately 36 kDa. The bacteriocin was sensitive to pepsin, protease, and pancreatin, and was inactivated by heating at 65 °C for 1 h. Simulating in vitro avian digestion decreased the antagonistic activity by 74.7%, but the addition of 1% bovin serum albumin restored 13% of the lost antagonistic activity. Following ion-exchange purification, the bacteriocin had sufficient antagonistic activity against five tested pathogenic strains, but the addition of a protectant is necessary for utilization of bacteriocin of R. albus 7 as an antibiotic alternative in animal feed.

Effect of backgrounding and transition diets on fecal concentration and strain types of commensalEscherichia coliin beef cattle

Su, R., Munns, K., Beauchemin, K. A., Schwartzkopf-Genswein, K., Jin-Quan, L., Topp, E. and Sharma, R. 2011. Effect of backgrounding and transition diets on fecal concentration and strain types of commensal Escherichia coli in beef cattle. Can. J. Anim. Sci. 91: 449–458. The aim of the study was to assess the effect of four different backgrounding diets [55% corn silage in combination with 40% of either temper rolled barley-grain, wheat dried distillers' grain, corn dried distillers' grain or millrun (dry matter basis)] and a transition diet containing increasing amount of concentrate (60 to 90%) on fecal Escherichia coli in feedlot heifers. Heifers were fed backgrounding forage based diets for 91 d and then were shifted to a transition diet for an additional 18 d. Strain characterization of E. coli (n=224) was carried out at time time points over 109 d and indicated that heifers fed the barley–grain diet shed higher (P<0.001) total and tetracycline-resistant (Tetr) E. coli in the backgrounding phase. Of the total E. coli examined (n=224), 70.3% showed resistance to one or more of the 14 antimicrobials examined, which increased to 82.3% by day 109. Among the recovered E. coli, 23 phenotypes and 154 pulsed field gel electrophoresis patterns grouped into 38 clusters indicative of extensive E. coli diversity in heifers. Although supplementation of 40% barley-grain was correlated to higher total E. coli shedding in the backgrounding phase, the backgrounding diets did not influence strain clustering. Strains collected during the transition phase clustered more closely than those collected during the backgrounding phase. This increased strain clustering with high concentrate inclusion in the transition diet was observed within 18 d of the transition phase. Our study indicated variations in E. coli shedding rates and strain clustering in relation to time and diet.

AS-48 bacteriocin: close to perfection

Bacteriocin AS-48 is an intriguing molecule because of its unique structural characteristics, genetic regulation, broad activity spectrum, and potential biotechnological applications. It was the first reported circular bacteriocin and has been undoubtedly the best characterized for the last 25 years. Thus, AS-48 is the prototype of circular bacteriocins (class IV), for which the structure and genetic regulation have been elucidated. This review discusses the state-of-the-art in genetic engineering with regard to this circular protein, with the use of site-directed mutagenesis and circular permutation. Mutagenesis studies have been used to unravel the role of (a) different residues in the biological activity, underlining the relevance of several residues involved in membrane interaction and the low correlation between stability and activity and (b) three amino acids involved in maturation, providing information on the specificity of the leader peptidase and the circularization process itself. To investigate the role of circularity in the stability and biological properties of the enterocin AS-48, two different ways of linearization have been attempted: in vitro by limited proteolysis experiments and in vivo by circular permutation in the structural gene as-48A. The results summarized here show the significance of circularization on the secondary structure, potency and, especially, the stability of AS-48 and point as well to a putative role of the leader peptide as a protecting moiety in the pre-proprotein. Taken all together, the data available on circular bacteriocins support the idea that AS-48 has been engineered by nature to make a remarkably active and stable protein with a broad spectrum of activity.

Characterization of garvicin ML, a novel circular bacteriocin produced by Lactococcus garvieae DCC43, isolated from mallard ducks (Anas platyrhynchos)

Lactococcus garvieae DCC43 produces a bacteriocin, garvicin ML (GarML), with a molecular mass of 6,004.2 Da. Data from de novo amino acid sequencing by tandem mass spectrometry and nucleotide sequencing by reverse genetics suggested that the bacteriocin is synthesized as a 63-amino-acid precursor with a 3-amino-acid leader peptide that is removed by cleavage. Subsequently, a covalent linkage between the N and C termini forms the mature version of this novel 60-amino-acid circular bacteriocin.

Insights into the functionality of the putative residues involved in enterocin AS-48 maturation

AS-48 is a 70-residue, α-helical, cationic bacteriocin produced by Enterococcus faecalis and is very singular in its circular structure and its broad antibacterial spectrum. The AS-48 preprotein consists of an N-terminal signal peptide (SP) (35 residues) followed by a proprotein moiety that undergoes posttranslational modifications to yield the mature and active circular protein. For the study of the specificity of the region of AS-48 that is responsible for maturation, three single mutants have been generated by site-directed mutagenesis in the as-48A structural gene. The substitutions were made just in the residues that are thought to constitute a recognition site for the SP cleavage enzyme (His-1, Met1) and in those involved in circularization (Met1, Trp70). Each derivative was expressed in the enterococcal JH2-2 strain containing the necessary native biosynthetic machinery for enterocin production. The importance of these derivatives in AS-48 processing has been evaluated on the basis of the production and structural characterization of the corresponding derivatives. Notably, only two of them (Trp70Ala and Met1Ala derivatives) could be purified in different forms and amounts and are characterized for their bactericidal activity and secondary structure. We could not detect any production of AS-48 in JH2-2(pAM401-81(His-1Ile)) by using the conventional chromatographic techniques, despite the high efficiency of the culture conditions applied to produce this enterocin. Our results underline the different important roles of the mutated residues in (i) the elimination of the SP, (ii) the production levels and antibacterial activity of the mature proteins, and (iii) protein circularization. Moreover, our findings suggest that His-1 is critically involved in cleavage site recognition, its substitution being responsible for the blockage of processing, thereby hampering the production of the specific protein in the cellular culture supernatant.

The use of PCR for the identification and characterisation of bacteriocin genes from bacterial strains isolated from rumen or caecal contents of cattle and sheep

PCR primers were designed to amplify the gene that encodes bovicin 255 from Streptococcus gallolyticus LRC0255 and the bacteriocin genes from Butyrivibrio fibrisolvens strains AR10 and OR79A (bviD and bvi79A) in order to screen for their incidence in rumen and caecal B. fibrisolvens and Streptococcus bovis-like isolates from New Zealand and North American ruminants. None of the B. fibrisolvens-like strains (n=34) isolated from New Zealand or North America had the genes encoding for butyrivibriocins AR10 (bviD) or OR79 (bvi79A). However, seven S. bovis isolates from New Zealand ruminants and three from North American animals had the bovicin 255 gene. Sequence comparison of cloned bovicin 255 PCR products indicated a 92.9-95.7% similarity to that of the corresponding bovicin 255 gene sequence of S. gallolyticus. Four of the New Zealand bovicin 255 positive S. bovis isolates were from the caecal contents of the same sheep and had identical PFGE profiles. Two other S. bovis isolates sharing the same PFGE profile were isolated from a separate animal from the same flock. PFGE analysis of the North American strains indicated that all three were closely related as two of three had identical PFGE profiles with the remaining isolate differing only by a single band position. The 16S rRNA gene sequences of the 10 isolates were at least 99.8% identical to S. bovis. All 10 S. bovis isolates having the gene for bovicin 255 produced bacteriocin activity that inhibited the growth of Peptostreptococcus anaerobius D1 in a deferred antagonism plating (DAP) assay. Certain S. bovis isolates obtained from ruminants have bacteriocin activity associated with a distinct bovicin 255 gene sequence but it appears that bacteriocin production by the rumen anaerobe B. fibrisolvens may be uncommon in strains isolated from cattle and sheep in New Zealand.

Uberolysin: a novel cyclic bacteriocin produced by Streptococcus uberis

Streptococcus uberis is commonly found in the environment and in association with various bovine body sites and is a major cause of bovine mastitis. Moreover, S. uberis is known to produce a variety of bacteriocin-like inhibitory substances, antimicrobial agents that generally inhibit closely related bacterial species. In this respect, S. uberis strain 42 has previously been shown to produce a novel nisin variant named nisin U. This paper reports that, in addition to nisin U, S. uberis strain 42 produces a second bacteriocin that induces the lysis of metabolically active, susceptible target bacteria and which has therefore been named uberolysin. Isolation of the native active antimicrobial agent revealed that uberolysin is a 7048 Da peptide that is refractory to sequence analysis by Edman degradation. Transposon mutagenesis was used to generate a uberolysin-negative mutant of S. uberis 42 and sequencing of DNA flanking the insertion site revealed, in addition to the structural gene (ublA), several open reading frames likely to be involved in post-translational modification, transport and producer self-protection (immunity), and possibly in regulation of the biosynthetic gene cluster. In addition, a pair of direct repeats that may be involved in bacteriocin acquisition were identified; indeed, ublA could be identified in 18 % of tested S. uberis strains. Enzymic hydrolysis of uberolysin was used to confirm that ublA does indeed encode the precursor of uberolysin, that an unusually short leader sequence of only six amino acids is cleaved during processing of the mature peptide and that uberolysin is post-translationally covalently modified to form a head-to-tail monocycle. Thus, uberolysin is a unique cyclic bacteriocin, belonging to the same family of bacteriocins as enterocin AS-48 and circularin A.

Screening of bacteria from the cattle gastrointestinal tract for inhibitory activity against enterohemorrhagic Escherichia coli O157:H7, O111:H-, and O26:H11

A quick and reproducible microgel plate assay was adapted to screen bacteria from cattle gastrointestinal tracts for production of compounds inhibitory to the growth of three enterohemorrhagic Escherichia coli (EHEC) serotypes: O157:H7, O111:H-, and O26:H11. The inhibitory activity of 309 bacteria, isolated on several agar media, was assessed by a microgel assay performed in 96-well microtiter plates. Fifty-three isolates secreted inhibitory compounds with a molecular weight of less than 1,000. In 12 isolates, the inhibitory activity was attributable to compounds other than lactic or acetic acid. These compounds were highly heat tolerant, with varying sensitivity to digestion by proteolytic enzymes. The inhibitory isolates were identified as lactic acid-producing bacteria on the basis of a combination of analyses, including 16S-rDNA restriction fragment length polymorphisms, 16S-rDNA gene sequences, and fermentation end products. The lactic acid bacteria of ruminants may contain antibacterial compounds not yet described. Naturally occurring populations of lactic acid bacteria may have potential as probiotics, to reduce the carriage of EHEC in the gastrointestinal tract of ruminants.

Effect of oral administration of Butyrivibrio fibrisolvens MDT-1 on experimental enterocolitis in mice

Butyrivibrio fibrisolvens MDT-1, a butyrate-producing strain, was evaluated for use as a probiotic to prevent enterocolitis. Oral administration of the MDT-1 strain (10(9) CFU/dose) alleviated the symptoms of colitis (including body weight loss, diarrhea, bloody stool, organic disorder, and mucosal damage) that are induced in mice drinking water that contains 3.0% dextran sulfate sodium. In addition, myeloperoxidase (MPO) activity levels in colonic tissue were reduced, suggesting that MDT-1 mitigates bowel inflammation. The addition of MDT-1 culture supernatant inhibited the growth of nine clinical isolates of Campylobacter jejuni and Campylobacter coli that could potentially cause enterocolitis. Infection of mice with C. coli 11580-3, one of the isolates inhibited by MDT-1 in vitro, resulted in diarrhea, mucosal damage, increased MPO activity levels in colonic tissue, increased numbers of C. coli in the cecum, and decreased body weight gain. However, administration of MDT-1 to mice, prior to and during C. coli infection, reduced these effects. These results suggest that Campylobacter-induced enterocolitis can be alleviated by using B. fibrisolvens as a probiotic.

Oral administration of butyrivibrio fibrisolvens, a butyrate-producing bacterium, decreases the formation of aberrant crypt foci in the colon and rectum of mice

Butyrivibrio fibrisolvens, a butyrate-producing ruminal bacterium, was evaluated for use as a probiotic to prevent colorectal cancer. Oral administration to Jcl:ICR mice of a new strain of B. fibrisolvens (MDT-1) that produces butyrate at a high rate (10(9) cfu/dose) increased the rate of butyrate production by fecal microbes, suggesting that MDT-1 can grow in the gut. The number of colorectal aberrant crypt foci (ACF), putative preneoplastic lesions induced by 1,2-dimethylhydrazine, was reduced after MDT-1 administration (10(9) cfu/dose, 3 times/wk for 4 wk). The number of aberrant crypts (ACs), number of foci having 3 or 4 ACs per focus, and the percentage of mice having 3 or 4 ACs per focus were also reduced, suggesting that the progress of lesions was suppressed by MDT-1. Interestingly, the MDT-1 cell homogenate did not have a similar beneficial effect. MDT-1 had low beta-glucuronidase activity, and administration of MDT-1 reduced the beta-glucuronidase activity in the colorectal contents. The numbers of natural killer (NK) and NKT cells in the spleen were markedly enhanced in response to MDT-1. Decreased beta-glucuronidase activity and increased numbers of NK and NKT cells and butyrate production may explain in part why MDT-1 administration suppressed ACF formation. These results suggest that colorectal cancer may be prevented or suppressed by the utilization of MDT-1 as a probiotic. Administration of MDT-1 had no harmful effect on the health of mice at least for 3 mo.

Effect of finishing diets on Escherichia coli populations and prevalence of enterohaemorrhagic E. coli virulence genes in cattle faeces

AIM

To determine the effect of different carbohydrate-based finishing diets on fermentation characteristics and the shedding of Escherichia coli and enterohaemorrhagic E. coli (EHEC) virulence genes in cattle faeces.

METHODS AND RESULTS

The size of faecal E. coli populations and fermentation characteristics were ascertained in three experiments where cattle were maintained on a range of finishing diets including high grain, roughage, and roughage + molasses (50%) diets. Increased E. coli numbers, decreased pH and enhanced butyrate and lactate fermentation pathways were associated with grain diets, whereas roughage and roughage + molasses diets resulted in decreased concentrations of ehxA, eaeA and stx(1) genes, this trend remaining at lairage. In one experiment, faecal E. coli numbers were significantly lower in animals fed roughage and roughage + molasses, than animals fed grain (4.5, 5.2 and 6.3 mean log10 g(-1) digesta respectively). In a second experiment, faecal E. coli numbers were 2 log lower in the roughage and roughage + molasses diets compared with grain-fed animals prior to lairage (5.6, 5.5 and 7.9 mean log10 g(-1) digesta respectively) this difference increasing to 2.5 log at lairage.

CONCLUSIONS

The type of dietary carbohydrate has a significant effect on E. coli numbers and concentration of EHEC virulence genes in faeces of cattle.

SIGNIFICANCE AND IMPACT OF THE STUDY

The study provides a better understanding of the impact finishing diet and commercial lairage management practices may have on the shedding of E. coli and EHEC virulence factors, thus reducing the risk of carcass contamination by EHEC.

Effect of environmental factors on production of lichenin, a chromosomally encoded bacteriocin-like compound produced by Bacillus licheniformis 26L-10/3RA

Effect of environmental factors on production of lichenin, a bacteriocin-like compound produced by Bacillus licheniformis 26L-10/3RA isolated from buffalo rumen was studied. Lichenin represents the first anaerobiosis-specific expression of broad-spectrum antibacterial compound effective only under anaerobic conditions. Production of lichenin by B. licheniformis 26L-10/3RA was found to be very high at 39 degrees C in L-10 medium supplemented with 0.5% glucose and 20% (w/v) inert thermocol beads. Lichenin production was highest at pH 6.8 after 72-96h of incubation. Our study also indicated that Lichenin is not a plasmid-linked characteristic and is encoded by chromosomal DNA. Results obtained can be used in large-scale production of Lichenin for potential application in manipulating rumen function intended for improving productivity of the ruminants.

Albusin B, a bacteriocin from the ruminal bacterium Ruminococcus albus 7 that inhibits growth of Ruminococcus flavefaciens

An approximately 32-kDa protein (albusin B) that inhibited growth of Ruminococcus flavefaciens FD-1 was isolated from culture supernatants of Ruminococcus albus 7. Traditional cloning and gene-walking PCR techniques revealed an open reading frame (albB) encoding a protein with a predicted molecular mass of 32,168 Da. A BLAST search revealed two homologs of AlbB from the unfinished genome of R. albus 8 and moderate similarity to LlpA, a recently described 30-kDa bacteriocin from Pseudomonas sp. strain BW11M1.

Butyrivibriocin AR10, a new cyclic bacteriocin produced by the ruminal anaerobe Butyrivibrio fibrisolvens AR10: characterization of the gene and peptide

The gene (bviA) encoding the ruminal bacteriocin butyrivibriocin AR10 was cloned from an EcoRI library by using an oligonucleotide probe based on a partial peptide sequence of the previously isolated peptide. The gene encoded an 80 amino acid prebacteriocin that demonstrated significant identity with the cyclic bacteriocin gassericin A. Negative ion time of flight mass spectroscopic analysis (ESI/MS) indicated a mass of 5981.5 Da for the isolated bacteriocin, a molecular mass that could not be generated by removal of a leader peptide alone. However, an N- to C-terminal cyclization of the predicted mature bacteriocin resulted in a peptide that conformed to the determined mass and charge characteristics. Northern blotting confirmed that expression of bviA mirrored the production of the bacteriocin in both liquid and solid media.

Opportunities to improve fiber degradation in the rumen: microbiology, ecology, and genomics

The degradation of plant cell walls by ruminants is of major economic importance in the developed as well as developing world. Rumen fermentation is unique in that efficient plant cell wall degradation relies on the cooperation between microorganisms that produce fibrolytic enzymes and the host animal that provides an anaerobic fermentation chamber. Increasing the efficiency with which the rumen microbiota degrades fiber has been the subject of extensive research for at least the last 100 years. Fiber digestion in the rumen is not optimal, as is supported by the fact that fiber recovered from feces is fermentable. This view is confirmed by the knowledge that mechanical and chemical pretreatments improve fiber degradation, as well as more recent research, which has demonstrated increased fiber digestion by rumen microorganisms when plant lignin composition is modified by genetic manipulation. Rumen microbiologists have sought to improve fiber digestion by genetic and ecological manipulation of rumen fermentation. This has been difficult and a number of constraints have limited progress, including: (a) a lack of reliable transformation systems for major fibrolytic rumen bacteria, (b) a poor understanding of ecological factors that govern persistence of fibrolytic bacteria and fungi in the rumen, (c) a poor understanding of which glycolyl hydrolases need to be manipulated, and (d) a lack of knowledge of the functional genomic framework within which fiber degradation operates. In this review the major fibrolytic organisms are briefly discussed. A more extensive discussion of the enzymes involved in fiber degradation is included. We also discuss the use of plant genetic manipulation, application of free-living lignolytic fungi and the use of exogenous enzymes. Lastly, we will discuss how newer technologies such as genomic and metagenomic approaches can be used to improve our knowledge of the functional genomic framework of plant cell wall degradation in the rumen.

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

Rumen bacterium Pseudobutyrivibrio xylanivorans strain Mz5T possessed a potent xylanolytic enzyme system consisting of at least 7 different xylan hydrolases with molar mass 27-145 kDa. Three of them were successfully isolated in active native form. This strain produced butyrate and lactate on different saccharides. cis-9, trans-11-Conjugated linoleic acid was also detected in the culture medium. Bacteriocin-like inhibitory substances of Mz5T were active against some strains of rumen bacteria and against selected Salmonella and E. coli isolates from poultry meat. The strain Mz5T retained viability and xylanolytic activity also under not fully anaerobic conditions; its cells attached to the Caco-2 cells so that its successful association with gut epithelial cells may be expected. These in vitro results confirmed several probiotic traits of the isolate Mz5T and justified further in vivo experiments to test its ability to improve animal health and performance.

Distribution of genes encoding the trypsin-dependent lantibiotic ruminococcin A among bacteria isolated from human fecal microbiota

Fourteen bacterial strains capable of producing a trypsin-dependent antimicrobial substance active against Clostridium perfringens were isolated from human fecal samples of various origins (from healthy adults and children, as well as from adults with chronic pouchitis). Identification of these strains showed that they belonged to Ruminococcus gnavus, Clostridium nexile, and Ruminococcus hansenii species or to new operational taxonomic units, all from the Clostridium coccoides phylogenetic group. In hybridization experiments with a probe specific for the structural gene encoding the trypsin-dependent lantibiotic ruminococcin A (RumA) produced by R. gnavus, seven strains gave a positive response. All of them harbored three highly conserved copies of rumA-like genes. The deduced peptide sequence was identical to or showed one amino acid difference from the hypothetical precursor of RumA. Our results indicate that the rumA-like genes have been disseminated among R. gnavus and phylogenetically related strains that can make up a significant part of the human fecal microbiota.

Bacteriocin-like activity of Butyrivibrio fibrisolvens JL5 and its effect on other ruminal bacteria and ammonia production

When ruminal bacteria from a cow fed hay were serially diluted into an anaerobic medium that had only peptides and amino acids as energy sources, little growth or ammonia production was detected at dilutions greater than 10(-6). The 10(-8) and 10(-9) dilutions contained bacteria that fermented carbohydrates, and some of these bacteria inhibited Clostridium sticklandii SR, an obligate amino acid-fermenting bacterium. Phylogenetic analysis indicated that the most active isolate (JL5) was closely related to Butyrivibrio fibrisolvens B835. Strain JL5 inhibited B. fibrisolvens 49 and a variety of other gram-positive organisms, but it had little effect on most gram-negative ruminal bacteria. Strain JL5 did not produce a bacteriocin-like inhibitory substance (BLIS) until it reached the late log or stationary phase. The JL5 BLIS did not cause the lysis of B. fibrisolvens 49, but the intracellular potassium level, the ATP level, the electrical potential, and the viability decreased rapidly. The JL5 BLIS also caused marked decreases in the viability and cellular potassium level of C. sticklandii SR. The membrane potential and intracellular ATP level also declined. The BLIS was degraded very slowly by pronase E, but it could be precipitated with 60% ammonium sulfate and dialyzed (3,500-Da cutoff). The BLIS could be separated from other peptides by polyacrylamide gel electrophoresis, and C. sticklandii SR overlays indicated that the molecular size of this compound was approximately 3,600 Da. Based on these results, it appeared that the JL5 BLIS was a pore-forming peptide. Because carbohydrate-fermenting ruminal bacteria could inhibit the growth of obligate amino acid-fermenting bacteria, BLIS may play a role in regulating ammonia production in vivo.

Isolation and characterization of enterocin BC25 and occurrence of the entA gene among ruminal gram-positive cocci

Enterocin BC25, a bacteriocin produced by Enterococcus faecium BC25 isolated from the rumen of cow was purified to homogeneity and sequenced. Twenty amino acids were identified in the peptide chain (TTHSGKYYGNGVYCT-KNKCT), identical to the N-terminal sequence of enterocin A. The DNA sequence of the enterocin BC25 structural gene and putative immunity protein exhibited high similarity to the entA gene. The occurrence of a 726 bp amplicon containing the enterocin A structural gene was studied among gram-positive ruminal cocci by PCR. Our results showed wide occurrence of the entA structural gene among ruminal enterococcal and streptococcal bacterial strains tested, and indicate variable ability to express bacteriocin production and resistance.

Presence of Butyrivibrio fibrisolvens in the digestive tract of dogs and cats, and its contribution to butyrate production

Numbers of Butyrivibrio fibrisolvens, a major butyrate-producing bacterium in the rumen, in feces of dogs and cats were estimated by competitive PCR. The type IIb of B. fibrisolvens, which produces much more lactate than butyrate, was detected at the levels (cells per g of feces dry weight) of 2.4x10(3)-9.0x10(5) for dogs and 1.7x10(4-)-6.2x10(5) for cats. However, the type I that produces much more butyrate than the type IIb was not detected in cat or dog feces (less than 6.0x10(4) cells per g of feces dry weight). Butyrate production by B. fibrisolvens type IIb in feces was estimated to be at most 30% of the butyrate production by mixed fecal microbes, which suggested that more butyrate is produced by microbes other than B. fibrisolvens in the intestines. Addition of B. fibrisolvens ATCC19171 (type I) to a culture of mixed fecal microbes increased butyrate production, and OB156 (type IIb) increased lactate production. When both the types were added, both the products were increased. Thus, introduction of both the types of B. fibrisolvens as a probiotic may increase butyrate and lactate production in the large intestine, which is possibly beneficial for the maintenance or improvement of the health of dogs and cats.

Bacteriocins of ruminal bacteria

Similar sequences of distribution of structural genes encoding enterocin A (isolated from the ruminal strain E. faecium BC25) and enterolysin A (isolated from the ruminal amylolytic strain S. bovis II/1) were demonstrated by PCR using oligonucleotide primers specific for these bacteriocins within the ruminal enterococcal and streptococcal strains. Variable occurrence of these bacteriocins was found within the populations of Gram-positive ruminal cocci.

Purification and characterization of a bacteriocin-like compound (Lichenin) produced anaerobically by Bacillus licheniformis isolated from water buffalo

AIMS

To characterize a bacteriocin-like factor from Bacillus licheniformis 26 L-10/3RA isolated from buffalo rumen.

METHODS AND RESULTS

The culture supernatant exhibited the antibacterial activity against a number of indicator organisms in a cut-well agar assay under anaerobic conditions. The inhibitory component was purified by following ammonium sulphate precipitation, gel filtration and ion exchange chromatography and confirmed to be a single peptide. A single band on tricine-sodium dodecyl sulphate-polyacrylamide gel electrophoresis confirmed that the peptide was purified to homogeneity and having an estimated molecular mass of approximately 1400 dalton. Complete amino acid sequence of the peptide yielded 12 amino acids from the N-terminal end (ISLEICXIFHDN). No homology with previously reported bacteriocins was observed and has been designated as Lichenin. Lichenin was found to be hydrophobic, sensitive to atmospheric oxygen, retained biological activity even after boiling for 10 min and was active over a pH range of 4.0-9.0.

CONCLUSIONS

The Lichenin represents the first anaerobiosis specific expression of bacteriocin-like compound isolated from Bacillus licheniformis 26 L-10/3RA of buffalo rumen origin.

SIGNIFICANCE AND IMPACT OF THE STUDY

Lichenin could be a potential candidate for manipulating the rumen function at molecular level intended for improving the productivity of the ruminant.

Ruminococcin A, a new lantibiotic produced by a Ruminococcus gnavus strain isolated from human feces

When cultivated in the presence of trypsin, the Ruminococcus gnavus E1 strain, isolated from a human fecal sample, was able to produce an antibacterial substance that accumulated in the supernatant. This substance, called ruminococcin A, was purified to homogeneity by reverse-phase chromatography. It was shown to be a 2,675-Da bacteriocin harboring a lanthionine structure. The utilization of Edman degradation and tandem mass spectrometry techniques, followed by DNA sequencing of part of the structural gene, allowed the identification of 21 amino acid residues. Similarity to other bacteriocins present in sequence libraries strongly suggested that ruminococcin A belonged to class IIA of the lantibiotics. The purified ruminococcin A was active against various pathogenic clostridia and bacteria phylogenetically related to R. gnavus. This is the first report on the characterization of a bacteriocin produced by a strictly anaerobic bacterium from human fecal microbiota.

Repeated ruminal dosing of Ruminococcus spp. does not result in persistence, but changes in other microbial populations occur that can be measured with quantitative 16S-rRNA-based probes

Digestibility of fibre in ruminants may be improved by the introduction of highly fibrolytic strains of ruminal bacteria. This approach may be feasible if, for example, strains of Ruminococcus that are significantly more fibrolytic than the normal population of Ruminococcus are used for inoculation purposes. Introduced strains of bacteria, irrespective of ecosystem, often decline after inoculation, and in this study, highly fibrolytic strains of Ruminococcus were continuously dosed to ensure that measurements of fibre digestion were made in the presence of significant numbers of the introduced bacteria. During dosing the total culturable count increased significantly (P<0.05), but declined post-dosing. The level of dosed Ruminococcus, and total Ruminococcus, Fibrobacter succinogenes and eukaryotes measured by 16S rRNA probes increased significantly (P<0.05) during the dosing period, but also declined post-dosing. When in vitro nylon bag digestibility, feed intake or whole-tract digestibility was measured, no improvement could be measured.

Expression of a modified Neocallimastix patriciarum xylanase in Butyrivibrio fibrisolvens digests more fibre but cannot effectively compete with highly fibrolytic bacteria in the rumen

AIMS

This study investigated the competitive abilities of two Neocallimastix patriciarum-derived xylanases constructs in Butyrivibrio fibrisolvens H17c (xynA and pUMSX) and their ability to compete in vivo.

METHODS AND RESULTS

The digestibility of neutral detergent fibre (NDF) increased during co-culture of xynA or pUMSX and weakly cellulolytic, but not with highly cellulolytic, ruminococci. Competition studies among xynA, pUMSX and cellulolytic consortia demonstrated that xynA was the fittest. XynA did not persist at high levels in the rumen and was undetectable after 22 days.

CONCLUSION

The construction of recombinant xylanolytic B. fibrisolvens does improve the digestibility of fibre above that of the native, but digestibility is still less than that of the most potent fibre digesters such as ruminococci.

SIGNIFICANCE AND IMPACT OF THE STUDY

Fibre digestion may be improved by genetic manipulation of ruminal bacteria but ecological parameters, such as persistence in vivo and the niche of the organism, must be taken into account.

Identification of bacteriocin-like inhibitors from rumen Streptococcus spp. and isolation and characterization of bovicin 255

Streptococci obtained from rumen sources were tested for the production of antibacterial compounds using a deferred-antagonism plating assay. Of 35 isolates tested, 7 were identified that inhibited the growth of other streptococci. None of the inhibitory activity was due to bacteriophage. Three isolates, LRC0253, LRC0255, and LRC0476, were selected for further characterization. Analysis of 16S ribosomal DNA indicated that LRC0476 was a strain of Streptococcus bovis, while isolates LRC0253 and LRC0255 are likely strains of Streptococcus gallolyticus. The antibacterial compounds produced by these bacteria were protease sensitive, remained active in a pH range from 1 to 12, and did not lose activity after heating at 100 degrees C for 15 min. The inhibitory peptide from strain LRC0255 was purified using pH-dependent adsorption and desorption to bacterial cells, followed by ammonium sulfate precipitation and reversed-phase chromatography and gel filtration. The peptide was 6 kDa, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. An oligonucleotide probe based on the N-terminal sequence of the purified peptide was used to identify the gene encoding the inhibitory peptide. The antibacterial peptide has characteristics that are very similar to those described for class II bacteriocins of gram-positive bacteria.