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Subacute ruminal acidosis (SARA) induces rumen dysbiosis, leading to LPS translocation and systemic immune activation. This study investigated the effects of a high-grain diet and intramammary LPS challenge on the milk microbiome of dairy cows. Cows were first fed a baseline control diet (day-7 to d-1; CON; 40% grain;\n                      <jats:italic>n<\/jats:italic>\n                      \u2009=\u200918). On d1, 12 cows were switched to a SARA diet (60% grain). On d30, six SARA (SARA_LPS) and the six CON cows (CON_LPS) were challenged intramammarily with LPS, while the other six SARA cows received a placebo (SARA_PLA). No CON_PLA group was enrolled. Milk samples were collected on d-2 (before feeding challenge), d30 (after feeding challenge; before LPS), and d32 (after LPS), and analysed using 16S rRNA gene amplicon sequencing and qPCR.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      During the feeding phases, more genera (70.1%) increased in CON than SARA cows, whereas more (65.3%) genera decreased their relative abundance in SARA compared to CON (\n                      <jats:italic>p<\/jats:italic>\n                      \u2009&lt;\u20090.001). This decline persisted in SARA_PLA cows, with more genera (62.4%) decreasing their abundance (\n                      <jats:italic>p<\/jats:italic>\n                      \u2009&lt;\u20090.001). However, LPS injection reversed the trend of the feeding effect, with more genera (79.3%) increasing in SARA_LPS cows in comparison to the other two groups, while more genera (85.5%) decreased in CON_LPS (\n                      <jats:italic>p<\/jats:italic>\n                      \u2009&lt;\u20090.001) in comparison to the other two groups. Alpha diversity correlated positively with bacterial cell equivalents. Of all genera, 22.1% correlated negatively with milk amyloid A (MAA), which increased post-LPS injection, 21.7% positively with lactose, and 13.4% positively with milk urea. SCC showed significant differences in beta-diversity, but no distinct visual clustering nor many correlations.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>The microbial dynamics suggest that high-grain diet and the LPS injection influence the milk bacterial community. More taxa correlated with MAA than with SCC, suggesting that MAA may better reflect immune-microbial interactions in milk. A roughage-rich diet promoted higher microbial abundance, whereas high-grain feeding reduced abundance over the timespan of 30\u2009days. Intramammary LPS challenge decreased absolute abundance in CON but increased it in SARA cows, suggesting a diet-dependent immune modulation of the mammary environment. These findings indicate that mammary gland epithelial integrity and immune mediators jointly shape the milk microbiome under metabolic and inflammatory stress.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s42523-025-00499-5","type":"journal-article","created":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T11:24:38Z","timestamp":1772105078000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Dynamics of the milk microbial community during subacute ruminal acidosis with or without intramammary lipopolysaccharide challenge in dairy cows"],"prefix":"10.1186","volume":"8","author":[{"given":"Viktoria","family":"Neubauer","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Siska","family":"Aditya","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Narciso M.","family":"Quijada","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefanie Urimare","family":"Wetzels","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Monika","family":"Dzieciol","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Poulad","family":"Pourazad","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qendrim","family":"Zebeli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Evelyne","family":"Selberherr","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,2,26]]},"reference":[{"key":"499_CR1","doi-asserted-by":"publisher","DOI":"10.4102\/jsava.v88i0.1465","author":"IM Petzer","year":"2017","unstructured":"Petzer IM, Karzis J, Donkin EF, Webb EC, Etter EMC. 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