Description of the microbiome of different segments of the gastrointestinal tract of healthy cows and comparison with cows with hemorrhagic bowel syndrome

Background: Hemorrhagic bowel syndrome (HBS), is an acute disease of ruminants characterized by bleeding in the jejunum. The blood clots eventually cause obstruction of the intestinal lumen, resulting in signs of colic, dilation of the abdomen and melena. The etiology of the disease remains unknown. Clostridium perfrigens type A has been isolated from cows with HBS and spoiled feed material. However , the role of Clostridia remains unclear as Clostridia spp. can also be isolated from healthy animals. Recently, the microbiome has received increasing attention in association with disease. The role of the gastrointestinal microbiome in relation to HBS has not been investigated. The objective of this study is to characterize the microbiome of healthy cows in different segments of the gastrointestinal tract and to compare the microbiome of healthy cows to cows with HBS in each gastrointestinal segment.Materials and Methods: Ingesta samples were collected from healthy cows from different gastrointestinal segments (rumen, omasum, abomasum, duodenum, proximal jejunum, distal jejunum, ileum, caecum, colon and rectum) after slaughter or euthanasia. Additionally samples were collected from the same locations from 5 cows with HBS. Next generation sequencing (Illumina) of the V4 region of the 16S RNA gene was used to assess the microbial composition from the ingesta.