Limosilactobacillus allomucosae sp. nov., a novel species isolated from wild boar faecal samples as a potential probiotic for domestic pigs.

Six strains, WILCCON 0050, WILCCON 0051, WILCCON 0052, WILCCON 0053, WILCCON 0054, WILCCON 0055, were isolated from four different faecal samples of wild boars on Pulau Ubin, Singapore, Singapore. Based on core genome phylogenetic analysis, the six strains formed a distinct clade within the genus Limosilactobacillus (Lm.), with the most closely related type strain being Lm.

Expanding the biosynthesis spectrum of hydroxy fatty acids: unleashing the potential of novel bacterial fatty acid hydratases.

Background: Hydroxy fatty acids represent an emerging class of compounds with promising applications in the chemical, medicinal and functional food sectors. The challenges associated with their chemical synthesis have spurred exploration of biological synthesis as an alternative route, particularly through the use of fatty acid hydratases. Fatty acid hydratases catalyse the regioselective addition of a hydrogen atom and a hydroxyl group from a water molecule to the carbon-carbon cis-double bond of unsaturated fatty acids to form hydroxy fatty acids.

Proposal for reclassification of the species as nom. nov. and transfer of the genus to the family .

X5-1 is an anaerobic, xylan-fermenting bacterium first isolated from methane-producing cattle manure. Initially identified as , this species was later reclassified as in 2019. Although this reclassification found support through Genome blast Distance Phylogeny analysis which placed X5-1 into the same clade as DSM 24995, it was contradicted by 16S rRNA gene phylogenetic analysis, which associated it with a set of misnamed species later reassigned into the genus .

sp. nov., a novel psychrotolerant species isolated from sauerkraut.

A Gram-stain-positive, rod-shaped, facultatively anaerobic and homofermentative strain, named WILCCON 0030, was isolated from sauerkraut (fermented cabbage) collected from a local market in the Moscow region of Russia. Comparative analyses based on 16S rRNA gene sequence similarity and whole genome relatedness indicated that strain WILCCON 0030 was most closely related to the type strains NCIMB 15186, LMG 31171 and LMG 31176. However, the average nucleotide identity and digital DNA-DNA hybridization prediction values with these closest relatives only ranged from 84.

Whole-Genome Sequence of Ligilactobacillus faecis WILCCON 0062, Isolated from Feces of a Wild Boar (Sus scrofa).

We report the whole genome of a strain of Ligilactobacillus faecis. The complete circular chromosome and plasmid of strain WILCCON 0062 were obtained through a combination of short- and long-read sequencing and may be used to derive unprecedented insights into the genome-level phylogeny and functional capacities of Ligilactobacillus faecis.

sp. nov., a novel species isolated from the wild ferment of a durian fruit ().

A Gram-stain-positive, rod-shaped, non-spore-forming, catalase-negative, urease-negative, homofermentative and facultatively anaerobic strain, named WILCCON 0076, was isolated from a wild ferment of pieces of a 'Kampung' durian fruit collected on the island of Ubin (Pulau Ubin), Singapore. The durian had fallen to the ground from a durian tree (), on which a group of long-tailed macaques had been observed picking and eating the fruits. Comparative analyses of 16S rRNA gene sequences indicated that WILCCON 0076 potentially represented a novel species within the genus , with the most closely related type strain being DSM 20509 (16S rRNA gene sequence similarity of 97.

Microbiome and Human Health: Current Understanding, Engineering, and Enabling Technologies.

The human microbiome is composed of a collection of dynamic microbial communities that inhabit various anatomical locations in the body. Accordingly, the coevolution of the microbiome with the host has resulted in these communities playing a profound role in promoting human health. Consequently, perturbations in the human microbiome can cause or exacerbate several diseases.

Genomic insights into the physiology of Quinella, an iconic uncultured rumen bacterium.

Quinella is a genus of iconic rumen bacteria first reported in 1913. There are no cultures of these bacteria, and information on their physiology is scarce and contradictory. Increased abundance of Quinella was previously found in the rumens of some sheep that emit low amounts of methane (CH) relative to their feed intake, but whether Quinella contributes to low CH emissions is not known.

Genome-wide high-throughput signal peptide screening via plasmid pUC256E improves protease secretion in Lactiplantibacillus plantarum and Pediococcus acidilactici.

Background: Proteases catalyze the hydrolysis of peptide bonds of proteins, thereby improving dietary protein digestibility, nutrient availability, as well as flavor and texture of fermented food and feed products. The lactobacilli Lactiplantibacillus plantarum (formerly Lactobacillus plantarum) and Pediococcus acidilactici are widely used in food and feed fermentations due to their broad metabolic capabilities and safe use. However, extracellular protease activity in these two species is low.

Resilience of Faecal Microbiota in Stabled Thoroughbred Horses Following Abrupt Dietary Transition between Freshly Cut Pasture and Three Forage-Based Diets.

The management of competition horses in New Zealand often involves rotations of short periods of stall confinement and concentrate feeding, with periods of time at pasture. Under these systems, horses may undergo abrupt dietary changes, with the incorporation of grains or concentrate feeds to the diet to meet performance needs, or sudden changes in the type of forage fed in response to a lack of fresh or conserved forage. Abrupt changes in dietary management are a risk factor for gastrointestinal (GI) disturbances, potentially due to the negative effects observed on the population of GI microbiota.

Seasonal Variation in the Faecal Microbiota of Mature Adult Horses Maintained on Pasture in New Zealand.

Seasonal variation in the faecal microbiota of forage-fed horses was investigated over a 12-month period to determine whether the bacterial diversity fluctuated over time. Horses ( = 10) were maintained on pasture for one year, with hay supplemented from June to October. At monthly intervals, data were recorded on pasture availability and climate (collected continuously and averaged on monthly basis), pasture and hay samples were collected for nutrient analysis, and faecal samples were collected from all horses to investigate the diversity of faecal microbiota using next-generation sequencing on the Illumina MiSeq platform.

Effects of long-acting, broad spectra anthelmintic treatments on the rumen microbial community compositions of grazing sheep.

Anthelmintic treatment of adult ewes is widely practiced to remove parasite burdens in the expectation of increased ruminant productivity. However, the broad activity spectra of many anthelmintic compounds raises the possibility of impacts on the rumen microbiota. To investigate this, 300 grazing ewes were allocated to treatment groups that included a 100-day controlled release capsule (CRC) containing albendazole and abamectin, a long-acting moxidectin injection (LAI), and a non-treated control group (CON).

Phylotype-Level Characterization of Complex Communities of Lactobacilli Using a High-Throughput, High-Resolution Phenylalanyl-tRNA Synthetase () Gene Amplicon Sequencing Approach.

The lactobacilli identified to date encompass more than 270 closely related species that were recently reclassified into 26 genera. Because of their relevance to industry, there is a need to distinguish between closely related and yet metabolically and regulatory distinct species, e.g.

A restriction enzyme reduced representation sequencing approach for low-cost, high-throughput metagenome profiling.

Microbial community profiles have been associated with a variety of traits, including methane emissions in livestock. These profiles can be difficult and expensive to obtain for thousands of samples (e.g.

Assessment of the Accuracy of High-Throughput Sequencing of the ITS1 Region of Neocallimastigomycota for Community Composition Analysis.

Anaerobic fungi (Neocallimastigomycota) are common inhabitants of the digestive tract of large mammalian herbivores, where they make an important contribution to plant biomass degradation. The internal transcribed spacer 1 (ITS1) region is currently the molecular marker of choice for anaerobic fungal community analysis, despite its known size polymorphism and heterogeneity. The aim of this study was to assess the accuracy of high-throughput sequencing of the ITS1 region of anaerobic fungi for community composition analysis.

Anaerobic fungal communities differ along the horse digestive tract.

Anaerobic fungi are potent fibre degrading microbes in the equine hindgut, yet our understanding of their diversity and community structure is limited to date. In this preliminary work, using a clone library approach we studied the diversity of anaerobic fungi along six segments of the horse hindgut: caecum, right ventral colon (RVC), left ventral colon (LVC), left dorsal colon (LDC), right dorsal colon (RDC) and rectum. Of the 647 ITS1 clones, 61.

PCR and Omics Based Techniques to Study the Diversity, Ecology and Biology of Anaerobic Fungi: Insights, Challenges and Opportunities.

Anaerobic fungi (phylum Neocallimastigomycota) are common inhabitants of the digestive tract of mammalian herbivores, and in the rumen, can account for up to 20% of the microbial biomass. Anaerobic fungi play a primary role in the degradation of lignocellulosic plant material. They also have a syntrophic interaction with methanogenic archaea, which increases their fiber degradation activity.

The Effects of Weaning Methods on Gut Microbiota Composition and Horse Physiology.

Weaning has been described as one of the most stressful events in the life of horses. Given the importance of the interaction between the gut-brain axis and gut microbiota under stress, we evaluated (i) the effect of two different weaning methods on the composition of gut microbiota across time and (ii) how the shifts of gut microbiota composition after weaning affect the host. A total of 34 foals were randomly subjected to a progressive (P) or an abrupt (A) weaning method.

Key Ecological Roles for Zoosporic True Fungi in Aquatic Habitats.

The diversity and abundance of zoosporic true fungi have been analyzed recently using fungal sequence libraries and advances in molecular methods, such as high-throughput sequencing. This review focuses on four evolutionary primitive true fungal phyla: the Aphelidea, Chytridiomycota, Neocallimastigomycota, and Rosellida (Cryptomycota), most species of which are not polycentric or mycelial (filamentous), rather they tend to be primarily monocentric (unicellular). Zoosporic fungi appear to be both abundant and diverse in many aquatic habitats around the world, with abundance often exceeding other fungal phyla in these habitats, and numerous novel genetic sequences identified.

Rumen metagenome and metatranscriptome analyses of low methane yield sheep reveals a Sharpea-enriched microbiome characterised by lactic acid formation and utilisation.

Background: Enteric fermentation by farmed ruminant animals is a major source of methane and constitutes the second largest anthropogenic contributor to global warming. Reducing methane emissions from ruminants is needed to ensure sustainable animal production in the future. Methane yield varies naturally in sheep and is a heritable trait that can be used to select animals that yield less methane per unit of feed eaten.

Natural variation in methane emission of sheep fed on a lucerne pellet diet is unrelated to rumen ciliate community type.

Only limited information is available on the roles of different rumen ciliate community types, first described by Eadie in 1962, in enteric methane (CH4) formation by their ruminant hosts. If the different types were differentially associated with CH4 formation, then ciliate community typing could be used to identify naturally high and low CH4-emitting animals. Here we measured the CH4 yields [g CH4 (kg feed dry matter intake, DMI)(-1)] of 118 sheep fed a standard pelleted lucerne diet at two different times, at least 2 weeks apart.

An adhesin from hydrogen-utilizing rumen methanogen Methanobrevibacter ruminantium M1 binds a broad range of hydrogen-producing microorganisms.

Symbiotic associations are ubiquitous in the microbial world and have a major role in shaping the evolution of both partners. One of the most interesting mutualistic relationships exists between protozoa and methanogenic archaea in the fermentative forestomach (rumen) of ruminant animals. Methanogens reside within and on the surface of protozoa as symbionts, and interspecies hydrogen transfer is speculated to be the main driver for physical associations observed between the two groups.