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To understand GM dynamics during malnutrition and subsequent re-feeding, we used a piglet model with a malnutrition-induced phenotype similar to humans. Piglets were weaned at the age of 4\u2009weeks, fed a nutritionally optimal diet for 1\u2009week post-weaning before being fed a pure maize diet for 7\u2009weeks to induce symptoms of malnutrition. After malnourishment, the piglets were re-fed using different regimes all based on general food aid products, namely Corn-Soy blend (CSB) fortified with phosphorus (CSB+), CSB fortified with phosphorus and skim milk powder (CSB++) and CSB fortified with phosphorus and added whey permeate (CSB\u2009+\u2009P).<\/jats:p>\n<\/jats:sec><jats:sec>\n<jats:title>Results<\/jats:title>\n<jats:p>Malnourishment had profound impact on the GM of the piglets leading to a less diverse GM dominated especially by <jats:italic>Akkermansia<\/jats:italic> spp. as determined by 16S rRNA gene amplicon sequencing. All three re-feeding regimes partly restored GM, leading to a more diverse GM compositionally closer to that of well-nourished piglets. This effect was even more pronounced for CSB++ compared to CSB+ and CSB\u2009+\u2009P.<\/jats:p>\n<\/jats:sec><jats:sec>\n<jats:title>Conclusion<\/jats:title>\n<jats:p>The GM of piglets were profoundly disturbed by malnourishment resulting in significantly increased abundance of <jats:italic>Akkermansia<\/jats:italic> spp. CSB++ may have superior effect on recovering GM diversity compared to the two other food aid products used in this study.<\/jats:p>\n<\/jats:sec>","DOI":"10.1186\/s12866-019-1658-5","type":"journal-article","created":{"date-parts":[[2019,12,10]],"date-time":"2019-12-10T11:04:07Z","timestamp":1575975847000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["Severe gut microbiota dysbiosis caused by malnourishment can be partly restored during 3\u2009weeks of refeeding with fortified corn-soy-blend in a piglet model of childhood malnutrition"],"prefix":"10.1186","volume":"19","author":[{"given":"Bingfeng","family":"Leng","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria B.","family":"S\u00f8rensen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Witold","family":"Kot","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas","family":"Thymann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lukasz","family":"Krych","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8121-1114","authenticated-orcid":false,"given":"Dennis S.","family":"Nielsen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2019,12,10]]},"reference":[{"issue":"9","key":"1658_CR1","first-page":"1369","volume":"67","author":"S Ahsan","year":"2017","unstructured":"Ahsan S, Mansoori N, Mohiuddin SM, Mubeen SM, Saleem R, Irfanullah M. 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