The bacteriophages of ruminal prevotellas

A review of bacteriophage and their application in domestic animals in a post-antibiotic era

Bacteriophages (phages for short) are the most abundant biological entities on Earth and are natural enemies of bacteria. Genomics and molecular biology have identified subtle and complex relationships among phages, bacteria and their animal hosts. This review covers composition, diversity and factors affecting gut phage, their lifecycle in the body, and interactions with bacteria and hosts. In addition, research regarding phage in poultry, aquaculture and livestock are summarized, and application of phages in antibiotic substitution, phage therapy and food safety are reviewed.

Prevotella diversity, niches and interactions with the human host

The genus Prevotella includes more than 50 characterized species that occur in varied natural habitats, although most Prevotella spp. are associated with humans. In the human microbiome, Prevotella spp. are highly abundant in various body sites, where they are key players in the balance between health and disease. Host factors related to diet, lifestyle and geography are fundamental in affecting the diversity and prevalence of Prevotella species and strains in the human microbiome. These factors, along with the ecological relationship of Prevotella with other members of the microbiome, likely determine the extent of the contribution of Prevotella to human metabolism and health. Here we review the diversity, prevalence and potential connection of Prevotella spp. in the human host, highlighting how genomic methods and analysis have improved and should further help in framing their ecological role. We also provide suggestions for future research to improve understanding of the possible functions of Prevotella spp. and the effects of the Western lifestyle and diet on the host-Prevotella symbiotic relationship in the context of maintaining human health.

Rumen Virus Populations: Technological Advances Enhancing Current Understanding

The rumen contains a multi-kingdom, commensal microbiome, including protozoa, bacteria, archaea, fungi and viruses, which enables ruminant herbivores to ferment and utilize plant feedstuffs that would be otherwise indigestible. Within the rumen, virus populations are diverse and highly abundant, often out-numbering the microbial populations that they both predate on and co-exist with. To date the research effort devoted to understanding rumen-associated viral populations has been considerably less than that given to the other microbial populations, yet their contribution to maintaining microbial population balance, intra-ruminal microbial lysis, fiber breakdown, nutrient cycling and genetic transfer may be highly significant. This review follows the technological advances which have contributed to our current understanding of rumen viruses and drawing on knowledge from other environmental and animal-associated microbiomes, describes the known and potential roles and impacts viruses have on rumen function and speculates on the future directions of rumen viral research.

Redirecting rumen fermentation to reduce methanogenesis

Methane production in ruminants has received global attention in relation to its contribution to the greenhouse gas effect and global warming. In the last two decades, research programs in Europe, Oceania and North America have explored a variety of approaches to redirecting reducing equivalents towards other reductive substrates as a means of decreasing methane production in ruminants. Some approaches such as vaccination, biocontrols (bacteriophage, bacteriocins) and chemical inhibitors directly target methanogens. Other approaches, such as defaunation, diet manipulations including various plant extracts or organic acids, and promotion of acetogenic populations, seek to lower the supply of metabolic hydrogen to methanogens. The microbial ecology of the rumen ecosystem is exceedingly complex and the ability of this system to efficiently convert complex carbohydrates to fermentable sugars is in part due to the effective disposal of H2 through reduction of CO2 to methane by methanogens. Although methane production can be inhibited for short periods, the ecology of the system is such that it frequently reverts back to initial levels of methane production though a variety of adaptive mechanisms. Hydrogen flow in the rumen can be modelled stoichiometrically, but accounting for H2 by direct measurement of reduced substrates often does not concur with the predictions of stoichiometric models. Clearly, substantial gaps remain in our knowledge of the intricacies of hydrogen flow within the ruminal ecosystem. Further characterisation of the fundamental microbial biochemistry of hydrogen generation and methane production in the rumen may provide insight for development of effective strategies for reducing methane emissions from ruminants.

Systematics and evolution of ruminal species of the genus Prevotella

Bacterial species of the genus Prevotella represent a numerically dominant microbial population in the rumen of cattle. They belong to the phylogenetic division Cytophaga-Flexibacter-Bacteroides (CFB) which is a large group of ecologically diverse bacteria with only a few shared traits. The phylogenetic descent from a common ancestor seems to be unquestionable, however, as judged from the small subunit ribosomal RNA analysis. Only 4 ruminal Prevotella species have been described to date, even though the sequence analysis of directly retrieved 16S rRNA genes indicates a large genetic diversity within this group of rumen bacteria. The closest relatives of ruminal Prevotella spp. are not surprisingly other species of the genus Prevotella, typically inhabiting the gastrointestinal tract, oral cavity and genital areas of other animals and man. The previous phylogenetic analysis showed that species of the genus Prevotella can be split into two groups or superclusters, the "ruminal" and the "non-ruminal prevotellas". One of 4 currently described ruminal Prevotella spp., i.e. P. albensis, has been placed outside the supercluster containing ruminal Prevotella spp. and within the supercluster containing the non-ruminal Prevotella spp. However, the number of available small subunit rRNA sequences from this species represents only a fraction of all known ruminal Prevotella sequences.

The bacteriophages of ruminal prevotellas

Rumen bacteriophage-lyzed bacterial strains of the genus Prevotella were isolated and preliminarily characterized. The strain TCl-1 the species P. bryantii was the only prevotella strain successfully infected with filter sterilized rumen fluid from a black-and-white Holstein cow. Two types of plaques were observed, both rather small and turbid. Preliminary electron microscopy observation showed that several morphologically different bacteriophages were present in these plaques. The plaque eluates were further used for the infection of other prevotella strains. The plaques produced by the bacteriophages were observed with two strains, i.e. P. bryantii B(1)4 and P. brevis GA33. The bacteriophages from both strains were examined by transmission electron microscopy and several morphologically different bacteriophages were observed, among others also a large virion with an icosahedral head with the diameter of approximately 120 nm. The bacteriophage was identified in plaques of bacterial cells of the strain GA33 and has an approximately 800 nm long helical tail, which places it among the largest ruminal bacteriophages described to date. Other bacteriophages from the same indicator strain as well as from P. bryantii B(1)4 strain were smaller and tail structures were not observed in all of them.