ORIGINAL RESEARCH article
Front. Anim. Sci.
Sec. Animal Nutrition
Pig feed as source for bacterial DNA and its potential impact on porcine gut microbiota studies
Provisionally accepted
- University of Veterinary Medicine Vienna, Vienna, Austria
Select one of your emails
You have multiple emails registered with Frontiers:
Notify me on publication
Please enter your email address:
If you already have an account, please login
You don't have a Frontiers account ? You can register here
Aside from being a source of energy and nutrients, pig's diet is also a source of microbial DNA, which may be a confounding factor in porcine gut microbiota studies based on DNA sequencing. Therefore, the present small-scale pilot study aimed to investigate gene copy numbers, diversity and taxonomic composition of bacterial DNA present in complete feeds for sows and piglets, including gestation, lactation and prestarter diets and a milk replacer, and to compare the bacterial communities in the feeds for piglets with those in gastric digesta of piglets consuming these feeds. Total DNA was extracted from the feed and gastric samples of piglets for 16S rRNA gene amplicon (V3-V4 region) sequencing. The results show that the feeds carried a high amount of bacterial DNA, ranging from 8.3 to 9.0 log10 gene copies/gram feed. Beta-diversity analysis further indicated clear separation between the bacterial communities in the cereal-based gestation, lactation and prestarter diets, and the milk replacer, whereas alpha-diversity was similar among feeds. Taxonomic evaluation demonstrated that cereal-based feeds were dominated by Pantoea, Pseudomonas, Paenibacillus and Erwinia, making up 41 to 68% of all reads, whereas the milk replacer was dominated by Streptococcus and Lactococcus with 57.4 and 13.2% relative abundance, respectively. Comparison of the bacterial communities in feed to those in gastric digesta of piglets on day 3, 7, 14, 21, 28, 31 and 35 of life showed that, although mostly low abundant, many taxa found in the feed were detectable in gastric digesta. A comparison at species level is more appropriate to estimate the proportional share of bacteria in the feed to the total bacterial DNA in gastric digestion. Overall, the present data provide valuable insight into the bacterial DNA load and diversity in pig feeds and demonstrate that the bacterial DNA found in gastric digesta may be influenced to a small degree by bacteria from the feed.
Keywords: Bacterial DNA, milk replacer, cereal-based diets, pig feed, microbiota
Received: 22 Sep 2025; Accepted: 04 Nov 2025.
Copyright: © 2025 Hartinger, Lerch, Yosi, Vötterl and Metzler-Zebeli. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Barbara Metzler-Zebeli, barbara.metzler@vetmeduni.ac.at
Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.