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

Abstract

Diet selection by grazing livestock may affect animal performance as well as the biodiversity of grazed areas. Recent DNA barcoding techniques allow to assess dietary plant composition in faecal samples, which may be additionally integrated by the description of gut microbiota. In this high throughput metabarcoding study, we investigated the diversity of plant, fungal and bacterial taxa in faecal samples of lactating cows of two breeds grazing an Alpine semi-natural grassland during summer. The estimated plant composition of the diet comprised 67 genera and 39 species, which varied remarkably during summer, suggesting a decline of the diet forage value with the advancing of the vegetative season. The fungal community included Neocallimastigomycota gut symbionts, but also Ascomycota and Basidiomycota plant parasite and coprophilous taxa, likely ingested during grazing. The proportion of ingested fungi was remarkably higher than in other studies, and varied during summer, although less than that observed for plants. Some variation related to breed was also detected. The gut bacterial taxa remained stable through the summer but displayed a breed-specific composition. The study provided insights in the reciprocal organisms’ interactions affecting, and being affected by, the foraging behaviour: plants showed a high temporal variation, fungi a smaller one, while bacteria had practically none; conversely, the same kingdoms showed the opposite gradient of variation as respect to the animal host breed, as bacteria revealed to be the group mostly characterized by host-specificity.

Animal board invited review: Grassland-based livestock farming and biodiversity

“…One reason that data on diet composition in free-ranging grazing livestock are comparatively limited is that methodologies for determining this, such as visual observation, faecal cuticle analysis ( Cuartas et al, 2000 ) and n-alkane analysis ( Ali et al, 2004 ), have been comparatively limited in their accuracy and/or are costly in terms of time and money. More recently, high-throughput next-generation sequencing technologies have emerged as a means of determining diet composition ( Pompanon et al, 2012 ), and DNA meta-barcoding offers considerable potential as a non-invasive rapid molecular technique to determine diet composition of both wild and domesticated herbivores ( Garnick et al, 2018 , Palumbo et al, 2021 ). However, this analytical approach still has limitations due to biological factors and technical issues that have the potential to influence the end sequencing results and resolution of taxonomic identification ( Lamb et al, 2019 ).…”

Gut Microbiome Studies in Livestock: Achievements, Challenges, and Perspectives

“…The majority of gut microbiome studies in cattle have focused on the characterization of microbial communities by 16S rRNA gene amplicon sequencing as a consequence of different animal diet composition [ 44 , 45 ], gastrointestinal tract (GIT) location [ 46 ], feed efficiency [ 47 ], breed-specificity [ 48 ], metabolic disturbs [ 49 ], changes over time [ 50 ] and individual specificities [ 51 , 52 ], as well as across housing types and farms [ 53 ]. Interestingly, special attention has been devoted to identifying individual-based differences irrespective of age, sex, breed, or environment [ 54 ], with patterns of similarity and dissimilarities helping to define the core microbiome in the bovine rumen [ 51 ] as well as other livestock [ 55 ].…”