In the duodenum, the bacterial populations differ considerably between the helminth-resistant and helminth-susceptible animals, perhaps helping to explain their different parasite burdens. Interestingly, there were no such differences between the groups in other sections of the GIT. The duodenum is the normal habitat for T. colubriformis in sheep  where this helminth is known to browse the mucosa and cause severe damage, including villus atrophy, crypt hyperplasia, and mucosal damage .
In the duodenum, alpha diversity values and bacterial richness were lower in the High-FEC group than in the Low-FEC group. In general ecological terms, greater diversity in a community indicates a more stable and favourable environment, suggesting that the duodenum of helminth-resistant sheep supports a better adapted microbiome which may make it difficult for the parasite to thrive. Thus in the helminth-susceptible sheep, can the lower diversity result in an unhealthy environment, i.e. different pH perhaps and/or a more inflamed duodenal mucosa, which will mean a more sustainable environment for the parasite. The lowest diversity values in the ileum indicates that the proliferation of micro-flora in the small intestine appears to be restricted, possibly by the high concentrations of bile, salts and digestive enzymes. The rumen-abomasum and large intestine (caecum, colon, faeces) maintained greater richness and diversity than the small intestine (duodenum, jejunum, ileum). Most nutrient digestion and absorption take place in the abomasum and small intestine , although some fermentation and absorption also occur in the caecum and colon .
Of the three phyla that dominated the duodenum of the helminth-resistant group, Firmicutes was the most abundant, in agreement with the observations by Wang et al  in small-tailed Han sheep. Indeed, the Firmicutes dominated the entire GIT, as seen in previous studies in ruminants [20, 21]. Firmicutes can digest fiber and cellulose and are therefore essential for ruminant fermentation . Other significant phyla in the duodenum of the helminth-resistant sheep were Chloroflexi and Elusimicrobia. The Chloroflexi is a complex and diverse group that includes anoxygenic photoautotrophs, aerobic chemoheterotrophs, and thermophilic and anaerobic organisms , many of which have been identified in environments as diverse as the human oral cavity, deep-sea sponges, and the sheep rumen [24, 25]. The Elusimicrobia actually contains a single class, the Endomicrobia, that includes numerous members found in the gut of termites and cockroaches, as well as the bovine rumen . Despite being present in the rumen, there is little information about their roles in the ruminant duodenum.
At genus level, 11 microorganisms were over-represented in the helminth-resistant group. Some of them have recently been taxonomically assigned, including Aminipila, Flexilinea, Lachnoclostridium, and Saccharofermentans. In brief, Aminipila, a novel genus isolated from cattle waste, has been associated with the degradation of L-arginine, L-lysine and L-serine, and the production of short-chain fatty acids, particularly acetate and butyrate . The genus Flexilinea, first reported in Holstein cows that were challenged with a live yeast supplement , is strictly anaerobic, requires yeast extract to grow, and ferments mainly carbohydrates . Interestingly, yeasts in the rumen have been shown to improve microbial establishment and the regulation of ruminal pH . Lachnoclostridium, a novel genus, includes a number of new species identified in the human gut in relation to colorectal tumorigenesis , but there is currently no information about their function in the sheep GIT. The novel genus Saccharofermentans, also dominant in the helminth-resistant group, is a specialist in fermentating sugar to produce acetic acid, lactate and fumarate, but cannot degrade cellulose . This genus has recently been identified in the rumen fluid of Chahaer lambs . Among the remaining bacteria associated with the helminth-resistant sheep, are genera that ferment mainly carbohydrates to produce butyrate, propionate and acetate [34–36]: Pseudobutyrivibrio and Succiniclasticum, previously identified in the cow rumen, and Elusimicrobium that was previously identified in the termite gut. Prevotella spp. also degrade protein and carbohydrates and they proliferate following infection by H. contortus and T. circumcincta in small ruminants [14, 37, 38]. These observations align with the increases in the abundance of this genus in helminth-resistant sheep in the present study. The changes in protein absorption included in the pathophysiological responses to helminth infection could elicit an increase in the abundance of Prevotella spp. . In humans, this genus has been found in people consuming strongly plant-based diets as well as those with chronic inflammatory diseases .
Bacterial abundance varied with GIT section, and substantial differences were observed among rumen-abomasum, small intestine and large intestine. Most common were: Eubacterium, a genus that includes a wide spectrum of species ; Oscillibacter, an abundant genus in the faeces of free-grazing sheep (although with low values in the jejunum and ileum) that is linked to the production of butyric acid and alpha-linolenic acid ; and Ruminococcus, a genus of cellulose degraders found in various species. These three genera belong to the Firmicutes phyla and most of them can decompose fibre and cellulose .
The bacterial populations that we identified as being promoted by helminth infiection are prominent in carbohydrate fermentation in the duodenum of helminth-resistant sheep. Our view is that worm-resistant sheep develop a compensatory mechanism in response to GIT parasites involving a marked disruption of the microbial flora . Bringing all of these observations together, it appears that a high parasite load increases protein loss and carbohydrate degradation at the site of helminth infection.