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Ruminant animals contribute significantly to the global value of agriculture and rely on a complex microbial community for efficient digestion. However, little is known of how this microbial-host relationship develops and is maintained. To begin to address this, we have determined the ability of three Bifidobacterium species isolated from the faeces of newborn calves to grow on carbohydrates typical of a newborn ruminant diet. Genome sequences have been determined for these bacteria with analysis of the genomes providing insights into the host association and identification of several genes that may mediate interactions with the ruminant gastrointestinal tract. The present study provides a starting point from which we can define the role of potential beneficial microbes in the nutrition of young ruminants and begin to influence the interactions between the microbiota and the host. The differences observed in genomic content hint at niche partitioning among the bifidobacterial species analysed and the different strategies they employ to successfully adapt to this habitat.

Recent research on the gastrointestinal microbiota of small ruminants, such as goats and sheep, has provided insights into their microbial ecology and its impact on health and productivity. The microbiota of small ruminants is diverse and includes bacteria, fungi, protozoa, and archaea, which play important roles in nutrient digestion, immune modulation, and overall gut health. The composition and functionality of the microbiota are influenced by diet, and changes in diet can affect animal performance and health. Understanding the microbiota-host interaction can shed light on how microbial dysbiosis contributes to diseases in small ruminants, while beneficial microbes can enhance resilience against pathogens and improve overall animal wellbeing. High-throughput sequencing technologies have revolutionized microbiota research in small ruminants, allowing for a comprehensive understanding of microbial communities and their responses to physiological and environmental changes. Probiotics and prebiotics are increasingly used to manipulate the gut microbiota composition in small ruminants, with the aim of improving nutrient utilization, immune responses, and overall gut health. Additionally, research has addressed the environmental impact of small ruminant farming practices on the composition and diversity of the gastrointestinal microbiota. Overall, understanding the gastrointestinal microbiota of small ruminants is crucial for optimizing their health, productivity, and welfare, as well as for developing sustainable farming practices. [Extracted from the article]

Abstract Background Streptococcus thermophilus represents the only species among the streptococci that has “Generally Regarded As Safe” status and that plays an economically important role in the fermentation of yogurt and cheeses. We conducted comparative genome analysis of S. thermophilus LMD-9 to identify unique gene features as well as features that contribute to its adaptation to the dairy environment. In addition, we investigated the transcriptome response of LMD-9 during growth in milk in the presence of Lactobacillus delbrueckii ssp. bulgaricus, a companion culture in yogurt fermentation, and during lytic bacteriophage infection. Results The S. thermophilus LMD-9 genome is comprised of a 1.8 Mbp circular chromosome (39.1% GC; 1,834 predicted open reading frames) and two small cryptic plasmids. Genome comparison with the previously sequenced LMG 18311 and CNRZ1066 strains revealed 114 kb of LMD-9 specific chromosomal region, including genes that encode for histidine biosynthetic pathway, a cell surface proteinase, various host defense mechanisms and a phage remnant. Interestingly, also unique to LMD-9 are genes encoding for a putative mucus-binding protein, a peptide transporter, and exopolysaccharide biosynthetic proteins that have close orthologs in human intestinal microorganisms. LMD-9 harbors a large number of pseudogenes (13% of ORFeome), indicating that like LMG 18311 and CNRZ1066, LMD-9 has also undergone major reductive evolution, with the loss of carbohydrate metabolic genes and virulence genes found in their streptococcal counterparts. Functional genome distribution analysis of ORFeomes among streptococci showed that all three S. thermophilus strains formed a distinct functional cluster, further establishing their specialized adaptation to the nutrient-rich milk niche. An upregulation of CRISPR1 expression in LMD-9 during lytic bacteriophage DT1 infection suggests its protective role against phage invasion. When co-cultured with L. bulgaricus, LMD-9 overexpressed genes involved in amino acid transport and metabolism as well as DNA replication. Conclusions The genome of S. thermophilus LMD-9 is shaped by its domestication in the dairy environment, with gene features that conferred rapid growth in milk, stress response mechanisms and host defense systems that are relevant to its industrial applications. The presence of a unique exopolysaccharide gene cluster and cell surface protein orthologs commonly associated with probiotic functionality revealed potential probiotic applications of LMD-9.

Lactobacillus gasseri ATCC 33323, Lactobacillus salivarius subsp. salivarius UCC 118 and Lactobacillus casei ATCC 334 contain one (LgaI), four (Sal1, Sal2, Sal3, Sal4) and one (Lca1) distinguishable prophage sequences, respectively. Several studies have revealed that these prophage sequences are narrowly distributed with lactobacilli.