Bacterial communities in the gastrointestinal tract segments of helminth-resistant and helminth-susceptible sheep

Erwin A Paz; Eng Guan Chua; Shamshad Ul Hassan; Johan C Greeff; Dieter G Palmer; Shimin Liu; Binit Lamichhane; Néstor Sepúlveda; Junhua Liu; Chin Yen Tay; Graeme B Martin

doi:10.1186/s42523-022-00172-1

Bacterial communities in the gastrointestinal tract segments of helminth-resistant and helminth-susceptible sheep

Anim Microbiome. 2022 Mar 14;4(1):23. doi: 10.1186/s42523-022-00172-1.

Authors

Erwin A Paz^{1

2}, Eng Guan Chua³, Shamshad Ul Hassan^{4

3}, Johan C Greeff^{4

5}, Dieter G Palmer⁵, Shimin Liu⁴, Binit Lamichhane³, Néstor Sepúlveda⁶, Junhua Liu⁷, Chin Yen Tay³, Graeme B Martin⁴

Affiliations

¹ UWA Institute of Agriculture, The University of Western Australia, Perth, 6009, Australia. erwin.pazmunoz@uwa.edu.au.
² CY O'Connor ERADE Village Foundation, P.O. Box 1, North Dandalup, WA, 6207, Australia. erwin.pazmunoz@uwa.edu.au.
³ Helicobacter Research Laboratory, The Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, 6009, Australia.
⁴ UWA Institute of Agriculture, The University of Western Australia, Perth, 6009, Australia.
⁵ Department of Primary Industries and Regional Development, South Perth, 6151, Australia.
⁶ Departamento de Produccion Agropecuaria, CTI-Carne-CEBIOR-BIOREN, Universidad de La Frontera, Av. Francisco Salazar 01145, Temuco, Chile.
⁷ College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.

Abstract

Background: Helminth parasitism is a world-wide problem in livestock industries, with major impacts on health, welfare and productivity. The role of the gut microbiota in host-helminth interactions in ruminants has been extensively examined and the present study added to this body of knowledge by assessing the effects of resistance and susceptibility to helminth infection in the gastro-intestinal tract (GIT). Australian Sheep Breeding Values (ASBVs) for faecal egg count (FEC) were used to select the 10 highly helminth-susceptible (High-FEC) and 10 highly helminth-resistant (Low-FEC) sheep. FEC status was confirmed during the experiment. Using samples from the faeces and the lumen of the rumen, abomasum, duodenum, jejunum, ileum, caecum, and colon, DNA was extracted and used for 16 rRNA gene amplicon sequencing.

Results: The most frequent genera identified along the GIT were Eubacterium, Oscillibacter, and Ruminococcus. Intersectoral-specialization zones were identified along the GIT, with the duodenum displaying major differences between the High-FEC and Low-FEC animals in values for alpha and beta diversity. After taking all samples into account and adjusting for GIT segment, the High-FEC and Low-FEC sheep differed significantly for four genera Butyrivibrio, Mycoplasma, Lachnoclostridium and Succiniclasticum. In the duodenum, the abundances of Aminipila, Lachnoclostridium and Mogibacterium differed significantly between the High-FEC and Low-FEC sheep. In the ileum, on the other hand, the genus Mycoplasma was significantly depleted in the Low-FEC group.

Conclusions: The gastro-intestinal microbial profile varies widely between helminth-resistant and helminth-susceptible sheep. Each GIT section appears to support a particular bacterial composition leading to inter-sectoral differences among the various microbial communities. The microbial populations were most rich and diverse in the duodenum of helminth-resistant sheep, comprising bacterial genera that generally ferment carbohydrates. This observation suggests that helminth-resistant sheep can reorganize the duodenal microbiome taxa which may restrict the development of parasites.

Keywords: 16S rRNA gene sequencing; Faecal-egg count; Helminth; Microbiome; Nematode; Sheep; Short-chain fatty acids.

Grants and funding

74160038/Postdoctoral fellowship CONICYT Chile