Terrestrial Vertebrate Animal Metagenomics, Non-domesticated Macropodidae, Kangaroo

This review will focus on current knowledge of the microbial ecosystems associated with a group of largely Australian macropod marsupials – the kangaroos. Kangaroos encompass a large and diverse group of grazing and browsing herbivores. The primary interest in their associated microbial ecosystems has revolved around nutrition and digestion. The macropod marsupials ferment feed material (plant biomass) in an enlarged pre-gastric chamber, the forestomach, prior to further digestion (Hume 1982). This chamber is functionally analogous to the rumen in ruminant livestock, but both groups of animals evolved separately and therefore with different microbial species filling similar niches, over many millions of years

Isolation and characterization of lytic phages fromBacterioides ruminicola ssbrevis

Two bacteriophages (phgrBrb01 and phgrBrb02), lytic toBacteroides ruminicola ssbrevis AR20, were isolated from sewage water. Both phages possessed polyhedral heads and long noncontractile tails, and were classified as Siphoviridae of morphotype B1. Bacteria resistant to phages phgrBrb01 and phgrBrb02 arose following lysis of broth cultures. Survivors of phgrBrb01 infection were capsulated but remained susceptible to phgrBrb02 infection. Survivors of phgrBrb02 infection were noncapsulated and were resistant to attack by both phgrBrb01 and phgrBrb02. Neither phage lysogenized the host. Both phages contained double-stranded DNA, and their restriction endonuclease digestion patterns indicated that the phage genomes were circularly permuted and terminally redundant. Phage phgrBrb01 genome was examined in greater detail and confirmed to be circularly permuted, of size 33 kb, with a terminal redundancy of 2 kb, or 6% of the length of the genome. Circularly permuted genomes in phages of rumen bacteria do not appear to have been reported previously. At present, there is considerable interest in the genetic manipulation of rumen bacteria. The characterization of the phages described herein provides the basic information required for their use in the construction of vectors for the transfer of genetic material

Microbial ecology of the equine hindgut during oligofructose-induced laminitis

Alimentary carbohydrate overload is a significant cause of laminitis in horses and is correlated with drastic shifts in the composition of hindgut microbiota. Equine hindgut streptococcal species (EHSS), predominantly Streptococcus lutetiensis, have been shown to be the most common microorganisms culturable from the equine caecum prior to the onset of laminitis. However, the inherent biases of culture-based methods are estimated to preclude up to 70% of the normal caecal microbiota. The objective of this study was to evaluate bacterial population shifts occurring in the equine caecum throughout the course of oligofructose-induced laminitis using several culture-independent techniques and to correlate these with caecal lactate, volatile fatty acid and degrees of polymerization 3–7 fructo-oligosaccharide concentrations. Our data conclusively show that of the total microbiota present in the equine hindgut, the EHSS S. lutetiensis is the predominant microorganism that proliferates prior to the onset of laminitis, utilizing oligofructose to produce large quantities of lactate. Population shifts in lactobacilli and Escherichia coli subpopulations occur secondarily to the EHSS population shifts, thus confirming that lactobacilli and coliforms have no role in laminitis. A large, curved, Gram-negative rod previously observed during the early phases of laminitis induction was most closely related to the Anaerovibrio genus and most likely represents a new, yet to be cultured, genus and species. Correlation of fluorescence in situ hybridization and quantitative real-time PCR results provide evidence supporting the hypothesis that laminitis is associated with the death en masse and rapid cell lysis of EHSS. If EHSS are lysed, liberated cellular components may initiate laminitis.Gabriel J Milinovich, Paul C Burrell, Christopher C Pollitt, Athol V Klieve, Linda L Blackall, Diane Ouwerkerk, Erika Woodland and Darren J Trot

Enhanced meat chicken productivity in response to the probiotic Bacillus amyloliquefaciens H57 is associated with the enrichment of microbial amino acid and vitamin biosynthesis pathways

AIMS: Sub-therapeutic use of antibiotics as a growth promoter in animal diets has either been banned or voluntarily withdrawn from use in many countries to help curb the emergence of antibiotic-resistant pathogens. Probiotics may be an alternative to antibiotics as a growth promoter. We investigated the effects of a novel probiotic strain, Bacillus amyloliquefaciens H57 (H57) on the performance and microbiome-associated metabolic potential. METHODS AND RESULTS: Broiler chickens were fed either sorghum- or wheat-based diets supplemented with the probiotic H57. The growth rate, feed intake, and feed conversion in supplemented birds were compared with those in non-supplemented control. Caecal microbial metabolic functions were studied with shotgun metagenomic sequencing. H57 supplementation significantly increased the growth rate and daily feed intake of meat chickens relative to the non-supplemented controls without any effect on feed conversion ratio. In addition, relative to the non-supplemented controls, gene-centric metagenomics revealed that H57 significantly altered the functional capacity of the caecal microbiome, with amino acid and vitamin synthesis pathways being positively associated with H57 supplementation. CONCLUSIONS: Bacillus amyloliquefaciens H57 improves the performance of meat chickens or broilers and significantly modifies the functional potential of their caecal microbiomes, with enhanced potential capacity for amino acid and vitamin biosynthesis

Investigation of the microbial metabolism of carbon dioxide and hydrogen in the kangaroo foregut by stable isotope probing

Kangaroos ferment forage material in an enlarged forestomach analogous to the rumen, but in contrast to ruminants, they produce little or no methane. The objective of this study was to identify the dominant organisms and pathways involved in hydrogenotrophy in the kangaroo forestomach, with the broader aim of understanding how these processes are able to predominate over methanogenesis. Stable isotope analysis of fermentation end products and RNA stable isotope probing (RNA-SIP) were used to investigate the organisms and biochemical pathways involved in the metabolism of hydrogen and carbon dioxide in the kangaroo forestomach. Our results clearly demonstrate that the activity of bacterial reductive acetogens is a key factor in the reduced methane output of kangaroos. In in vitro fermentations, the microbial community of the kangaroo foregut produced very little methane, but produced a significantly greater proportion of acetate derived from carbon dioxide than the microbial community of the bovine rumen. A bacterial operational taxonomic unit closely related to the known reductive acetogen Blautia coccoides was found to be associated with carbon dioxide and hydrogen metabolism in the kangaroo foregut. Other bacterial taxa including members of the genera Prevotella, Oscillibacter and Streptococcus that have not previously been reported as containing hydrogenotrophic organisms were also significantly associated with metabolism of hydrogen and carbon dioxide in the kangaroo forestomach.The ISME Journal advance online publication, 13 March 2014; doi:10.1038/ismej.2014.25