Network-based gut microbiome analysis in dogs

References

• Addinsoft 2020. XLSTAT statistical and data analysis solution. Boston, USA.
   Google Scholar
• Alessandri G, Milani C, Mancabelli L, Longhi G, Anzalone R, Lugli GA, Duranti S, Turroni F, Ossiprandi MC, van Sinderen D, et al. 2020. Deciphering the bifidobacterial populations within the canine and feline guy microbiota. Appl Environ Microbiol. 86(7):e02875-19.
   PubMed Web of Science ®Google Scholar
• Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto J-M, et al. 2011. Enterotypes of the human gut microbiome. Nature. 473(7346):174–180.
   PubMed Web of Science ®Google Scholar
• Ban Y, An L, Jiang H. 2015. Investigating microbial co-occurrence patterns based on metagenomic compositional data. Bioinformatics. 31(20):3322–3329.
   PubMed Web of Science ®Google Scholar
• Barberán A, Bates ST, Casamayor EO, Fierer N. 2012. Using network analysis to explore co-occurrence patterns in soil microbial communities. Isme J. 6(2):343–351.
   PubMed Web of Science ®Google Scholar
• Bäumler AJ, Sperandio V. 2016. Interactions between the microbiota and pathogenic bacteria in the gut. Nature. 535(7610):85–93.
   PubMed Web of Science ®Google Scholar
• Bermingham EN, Maclean P, Thomas DG, Cave NJ, Young W. 2017. Key bacterial families (clostridiaceae, erysipelotrichaceae and bacteroidaceae) are related to the digestion of protein and energy in dogs. PeerJ. 5(march):e3019.
   PubMedGoogle Scholar
• Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, et al. 2019. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 37(8):852–857.
   PubMed Web of Science ®Google Scholar
• Bruni N, Martello E, Fusi E, Meineri G, Giardini A. 2020. Study of faecal parameters and body condition in dogs with a diet supplemented with Lactobacillus acidophilus D2/CSL (CECT 4529). Ital J Anim Sci. 19(1):704–711.
   Web of Science ®Google Scholar
• Chaffron S, Rehrauer H, Pernthaler J, von Mering C. 2010. A global network of coexisting microbes from environmental and whole-genome sequence data. Genome Res. 20(7):947–959.
   PubMed Web of Science ®Google Scholar
• Cintio M, Scarsella E, Sgorlon S, Sandri M, Stefanon B. 2020. Gut microbiome of healthy and arthritic dogs. Veterinary Sciences. 7(3):92.
   PubMedGoogle Scholar
• David LA, Materna AC, Friedman J, Campos-Baptista MI, Blackburn MC, Perrotta A, Erdman SE, Alm EJ. 2014. Host lifestyle affects human microbiota on daily timescales. Genome Biol. 15(7):R89.
   PubMed Web of Science ®Google Scholar
• Deng P, Swanson KS. 2015. Gut microbiota of humans, dogs and cats: current knowledge and future opportunities and challenges. Br J Nutr. 113(S1):S6–S17.
   PubMed Web of Science ®Google Scholar
• Eickhoff MJ, Bassler BL. 2018. SnapShot: bacterial quorum sensing. Cell. 174(5):1328–1328.e1.
   PubMed Web of Science ®Google Scholar
• Estrada-Peña A, Cabezas-Cruz A, Pollet T, Vayssier-Taussat M, Cosson JF. 2018. High throughput sequencing and network analysis disentangle the microbial communities of ticks and hosts within and between ecosystems. Frontiers in Cellular and Infectious Microbiology. 8:236.
   PubMed Web of Science ®Google Scholar
• Forster GM, Stockman J, Noyes N, Heuberger AL, Broeckling CD, Bantle CM, Ryan EP. 2018. A comparative study of serum biochemistry, metabolome and microbiome parameters of clinically healthy, normal weight, overweight, and obese companion dogs. Top Companion Anim Med. 33(4):126–135.
   PubMed Web of Science ®Google Scholar
• Friedman J, Alm EJ. 2012. Inferring correlation networks from genomic survey data. PLOS Comput Biol. 8(9):e1002687.
   PubMed Web of Science ®Google Scholar
• Garcia-Mazcorro JF, Barcenas-Walls JR, Suchodolski JS, Steiner JM. 2017. Molecular assessment of the fecal microbiota in healthy cats and dogs before and during supplementation with fructo-oligosaccharides (FOS) and inulin using high-throughput 454-Pyrosequencing. PeerJ. 5(aprile):e3184.
   PubMedGoogle Scholar
• Hirano H, Takemoto K. 2019. Difficulty in inferring microbial community structure based on co-occurrence network approaches. BMC Bioinformatics. 20(1):329 doi:10.1186/s12859-019-2915-1. PMC: 31195956
   PubMedGoogle Scholar
• Layeghifard M, Hwang DM, Guttman DS. 2017. Disentangling interactions in the microbiome: A network perspective. Trends Microbiol. 25(3):217–228. doi:10.1016/j.tim.2016.11.008.
   PubMed Web of Science ®Google Scholar
• Ling Z, Li Z, Liu X, Cheng Y, Luo Y, Tong X, Yuan L, Wang Y, Sun J, Li L, et al. 2014. Altered fecal microbiota composition associated with food allergy in infants. Appl Environ Microbiol. 80(8):2546–2554.
   PubMed Web of Science ®Google Scholar
• Loftus M, Al-Deen Hassouneh S, Yooseph S. 2021. Bacterial associations in the healthy human gut microbiome across populations. Sci Rep. 11(1):2828.
   PubMed Web of Science ®Google Scholar
• Lozupone CA, Faust K, Raes J, Faith JJ, Frank DN, Zaneveld J, Gordon JI, Knight R. 2012a. Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts. Genome Res. 22(10):1974–1984.
   PubMed Web of Science ®Google Scholar
• Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R. 2012b. Diversity, stability and resilience of the human gut microbiota. Nature. 489(7415):220–230.
   PubMed Web of Science ®Google Scholar
• Mandakovic D, Rojas C, Maldonado J, Latorre M, Travisany D, Delage E, Bihouée A, Jean G, Díaz FP, Fernández-Gómez B, et al. 2018. Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience. Sci Rep. 8(1):5875.
   PubMed Web of Science ®Google Scholar
• Mandal S, Van Treuren W, White RA, Eggesbø M, Knight R, Peddada SD. 2015. Analysis of composition of microbiomes: a novel method for studying microbial composition. Microb Ecol Health Dis. 26(1):27663.
   PubMedGoogle Scholar
• Markle JGM, Frank DN, Mortin-Toth S, Robertson CE, Feazel LM, Rolle-Kampczyk U, von Bergen M, McCoy KD, Macpherson AJ, Danska JS. 2013. Sex differences in the gut microbiome drive hormone-dependent regulation of autoimmunity. Science. 339(6123):1084–1088.
   PubMed Web of Science ®Google Scholar
• Muegge BD, Kuczynski J, Knights D, Clemente JC, González A, Fontana L, Henrissat B, Knight R, Gordon JI. 2011. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science. 332(6032):970–974.
   PubMed Web of Science ®Google Scholar
• Pacheco AR, Moel M, Segrè D. 2019. Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems. Nat Commun. 10(1):103.
   PubMedGoogle Scholar
• Pilla R, Suchodolski JS. 2019. The role of the canine gut microbiome and metabolome in health and gastrointestinal disease. Front Vet Sci. 6:498.
   PubMed Web of Science ®Google Scholar
• Ruan Q, Dutta D, Schwalbach MS, Steele JA, Fuhrman JA, Sun e F. 2006. Local similarity analysis reveals unique associations among marine bacterioplankton species and environmental factors. Bioinformatics. 22(20):2532–2538.
   PubMed Web of Science ®Google Scholar
• Sandri M, Manfrin C, Pallavicini A, Stefanon B. 2014. Microbial biodiversity of the liquid fraction of rumen content from lactating cows. Animal. 8(4):572–579.
   PubMed Web of Science ®Google Scholar
• Sandri M, Sgorlon S, Scarsella E, Stefanon B. 2020. Effect of different starch sources in a raw meat-based diet on fecal microbiome in dogs housed in a shelter. Animal Nutrition. 6(3):353–361.
   Web of Science ®Google Scholar
• Scarsella E, Cintio M, Iacumin L, Ginaldi F, Stefanon B. 2020a. Interplay between neuroendocrine biomarkers and gut microbiota in dogs supplemented with grape proanthocyanidins: results of dietary intervention study. Animals. 10(3):531.
   Web of Science ®Google Scholar
• Scarsella E, Stefanon B, Cintio M, Licastro D, Sgorlon S, Dal Monego S, Sandri M. 2020b. Learning machine approach reveals microbial signatures of diet and sex in Dog. PLOS One. 15(8):e0237874.
   PubMed Web of Science ®Google Scholar
• Schirmer M, Smeekens SP, Vlamakis H, Jaeger M, Oosting M, Franzosa EA, Ter Horst R, Jansen T, Jacobs L, Bonder MJ, et al. 2016. Linking the human gut microbiome to inflammatory cytokine production capacity. Cell. 167(4):1125–1136.e8.
   PubMed Web of Science ®Google Scholar
• Shaffer M, Thurimella K, Lozupone CA. 2020. SCNIC: sparse correlation network investigation for compositional data. 10.1101/2020.11.13.380733v1.
   Google Scholar
• Stachowicz JJ. 2001. Mutualism, facilitation, and the structure of ecological communities: positive interactions play a critical, but underappreciated, role in ecological communities by reducing physical or biotic stresses in existing habitats and by creating new habitats on which many species depend. BioScience. 51(3):235–246.
   Web of Science ®Google Scholar
• Suchodolski JS, Camacho J, Steiner JM. 2008. Analysis of bacterial diversity in the canine duodenum, jejunum, ileum, and colon by comparative 16S rRNA gene analysis. FEMS Microbiology Ecology. 66(3):567–578.
   PubMed Web of Science ®Google Scholar
• Thorburn AN, Macia L, Mackay CR. 2014. Diet, metabolites, and “western-lifestyle” inflammatory diseases. Immunity. 40(6):833–842.
   PubMed Web of Science ®Google Scholar
• Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. 2006. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. 444(7122):1027–1031.
   PubMed Web of Science ®Google Scholar
• Vastolo A, Riedmüller J, Cutrignelli MI, Zentek J. 2022. Evaluation of the effect of different dietary lipid sourses on dogs. Faecal Microbial Population and Activities. Animals. 12(11):1368.
   Google Scholar
• Zeng MY, Inohara N, Nuñez G. 2017. Mechanisms of inflammation-driven bacterial dysbiosis in the gut. Mucosal Immunol. 10(1):18–26.
   PubMed Web of Science ®Google Scholar