Bhosle A; Jackson MI; Walsh AM; Franzosa EA; Badri DV; Huttenhower C, 2024. Response of the gut microbiome and metabolome to dietary fiber in healthy dogs. Accepted at mSystems.
Nearing JT; Thompson KN; Louyakis AS; Bhosle A; Branck T; Badri DV; Franzosa EA; Brockel C; Huttenhower C; Short MI, 2024. Capturing Primer-Specific Ambiguity in Taxonomic Classification for Amplicon Sequencing. Under review.
Nearing JT; Kuntz T; Perdomo V; Nickols WA; Branck T; Bhosle A; Badri DV; Huttenhower C; Jackson MI; Thompson KN, 2025. Gut microbiome-metabolome interactions during varied low carbohydrate food consumption. Submitted for review.
Informative microbiome publications
Marco-Fuertes A; Marin C; Lorenzo-Rebenaque L; Vega S; Montoro-Dasi L, 2022. Antimicrobial Resistance in Companion Animals: A New Challenge for the One Health Approach in the European Union. Vet Sci 9. This review summarized AMR surveillance findings in several European countries and determined that AMR reporting was incomplete and inconsistent for companion animals, highlighting the need for integrated surveillance to be more inclusive of pets. Pets are potential reservoirs of AMR with possible transmission to humans and pet-inclusive reporting of AMR would further support the One Health concept.
Wernimont SM; Radosevich J; Jackson MI; Ephraim E; Badri DV; MacLeay JM; Jewell DE; Suchodolski JS, 2020. The Effects of Nutrition on the Gastrointestinal Microbiome of Cats and Dogs: Impact on Health and Disease. Front Microbiol 11:1266. This summary highlights the effects of pet owners’ food choices on the taxonomic composition of the gut microbiome, as well as on microbially-produced metabolites and their impact on pet health.
Coelho LP; Kultima JR; Costea PI; Fournier C; Pan Y; Czarnecki-Maulden G; Hayward MR; Forslund SK; Schmidt TSB; Descombes P; Jackson JR; Li Q; Bork P, 2018. Similarity of the dog and human gut microbiomes in gene content and response to diet. Microbiome 6(1):72. By creating an extensive gene catalog, researchers showed that the canine gut microbiome is more similar to the human gut microbiome compared to that of other mammals, likely due to shared environments and similar phenotypes among pets and their owners.
Lloyd-Price J; Mahurkar A; Rahnavard G; Crabtree J; Orvis J; Hall AB; Brady A; Creasy HH; McCracken C; Giglio MG; McDonald D; Franzosa EA; Knight R; White O; Huttenhower C, 2017. Strains, functions and dynamics in the expanded Human Microbiome Project.Nature 550(7674):61-66. Provides reference metagenomics for the body-wide human microbiome in a baseline population for comparison to other taxonomic, functional, and genetic profiles.
de Godoy MR; Hervera M; Swanson KS; Fahey GC Jr, 2016. Innovations in Canine and Feline Nutrition: Technologies for Food and Nutrition Assessment. Annu Rev Anim Biosci 4:311-33. This review discusses technologies for evaluating pet food quality and safety, along with methods like in vitro fermentation models of digestion and next-generation sequencing of microbial communities, which enable non-invasive assessment of nutritions’s impact on pet health.
