The structure of microbial populations in Nelore GIT reveals inter-dependency of methanogens in feces and rumen

Abstract

Background: The success of different species of ruminants in the colonization of a diverse range of environments is due to their ability to digest and absorb nutrients from cellulose, a complex polysaccharide found in leaves and grass. Ruminants rely on a complex and diverse microbial community, or microbiota, in a unique compartment known as the rumen to break down this polysaccharide. Changes in microbial populations of the rumen can affect the host's development, health, and productivity. However, accessing the rumen is stressful for the animal. Therefore, the development and use of alternative sampling methods are needed if this technique is to be routinely used in cattle breeding. To this end, we tested if the fecal microbiome could be used as a proxy for the rumen microbiome due to its accessibility. We investigated the taxonomic composition, diversity and interrelations of two different GIT compartments, rumen and feces, of 26 Nelore (Bos indicus) bulls, using Next Generation Sequencing (NGS) metabarcoding of bacteria, archaea and ciliate protozoa. Results: We identified 4265 Amplicon Sequence Variants (ASVs) from bacteria, 571 from archaea, and 107 from protozoa, of which 143 (96 bacteria and 47 archaea) were found common between both microbiomes. The most prominent bacterial phyla identified were Bacteroidetes (41.48%) and Firmicutes (56.86%) in the ruminal and fecal microbiomes, respectively, with Prevotella and Ruminococcaceae UCG-005 the most relatively abundant genera identified in each microbiome. The most abundant archaeal phylum identified was Euryarchaeota, of which Methanobrevibacter gottschalkii, a methanogen, was the prevalent archaeal species identified in both microbiomes. Protozoa were found exclusively identified in the rumen with Bozasella/ Triplumaria being the most frequent genus identified. Co-occurrence among ruminal and fecal ASVs reinforces the relationship of microorganisms within a biological niche. Furthermore, the co-occurrence of shared archaeal ASVs between microbiomes indicates a dependency of the predominant fecal methanogen population on the rumen population.

Screening of Microbes Associated With Swine Growth and Fat Deposition Traits Across the Intestinal Tract

“…In the current study, genus Alloprevotella positively related to host growth, which was consistent with the findings of Liu et al (2018), who suggested that a high abundance of Alloprevotella in the gut after feeding fucoidan can improve the physical health of mice such as by alleviating dyslipidemia. Previous studies have suggested that Ruminococcaceae UCG-005 also benefits the host by protecting against diabetes and elevating intestinal SCFA levels (Andrade et al, 2020). Wang et al (2018) found that the abundance of Ruminococcaceae UCG-005 was significantly reduced in the intestines of diarrheic goat kids compared with those of healthy goat kids.…”

Fecal and Ruminal Microbiome Components Associated With Methane Emission in Beef Cattle.

“…In our previous study, we extensively explored the taxonomic structure and relationships of bacteria, archaea and protozoa from two different sections of the Nelore cattle GIT [28] . Herein we expand this study by introducing a new experimental group under a different dietary treatment.…”

“…Herein, we will present only results concerning the taxonomic composition of dietary treatment group B. Please refer to [28] for an extensive exploration of the taxonomic diversity of the group A.…”

“…The GIT is a continuous and interconnected system, and as part of the digestive process, ruminants regurgitate digesta to chew partially digested material. Due to these characteristics, previous studies have suggested that the microbial populations of other sections of the GIT, such as both buccal and fecal environments, can be proxies for the rumen microbiome [28,68] . The ndings of these studies support the hypothesis of using these microorganisms as markers for the host's complex phenotypes, such as CH4 emission.…”

A multi-kingdom metabarcoding study on cattle grazing Alpine pastures discloses intra-seasonal shifts in plant selection and faecal microbiota

“…From the methodological standpoint, we chose to work with faeces in light of the following considerations. Although the compositions of rumen and faecal microbiota show a clear tract-specificity, they feature a high number of co-occurring taxa 44 , 67 – 69 ; moreover, faeces offer a practical and non-invasive shortcut to acquire extensive information on ruminant’s gut microbiome, which has been exploited in a number of the above cited studies 12 , 49 , 53 , 54 .…”