Microbiome sharing between children, livestock and household surfaces in western Kenya

PLoS ONE

Volumn 12, Issue 2, 2017, Pages

  Mosites, Emily ^a,b   Sammons, Matt ^b   Otiang, Elkanah ^c   Eng, Alexander ^a   Noecker, Cecilia ^a   Manor, Ohad ^a   Hilton, Sarah ^a   Thumbi, Samuel M ^b   Onyango, Clayton ^c   Garland Lewis, Gemina ^a   Call, Douglas R ^b   Njenga, M Kariuki ^b   Wasserheit, Judith N ^a   Zambriski, Jennifer A ^b   Walson, Judd L ^a,d   Palmer, Guy H ^b   Montgomery, Joel ^e   Borenstein, Elhanan ^a,f,g   Omore, Richard ^c   Rabinowitz, Peter M ^a,d  

^a UNIVERSITY OF WASHINGTON   (United States)

^b WASHINGTON STATE UNIVERSITY   (United States)

^c KENYA MEDICAL RESEARCH INSTITUTE   (Kenya)

^d UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^e CENTERS FOR DISEASE CONTROL AND PREVENTION   (United States)

^f University of Washington   (United States)

^g SANTA FE INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; RNA 16S;

ADULT; ARTICLE; BOVINE; CHICKEN; CHILD; COMMUNITY STRUCTURE; CONTROLLED STUDY; DEMOGRAPHY; DNA EXTRACTION; FEMALE; GENE AMPLIFICATION; GUT MICROBIOME; HUMAN; KENYA; LIVESTOCK; MAJOR CLINICAL STUDY; MALE; MICROBIOME; QUESTIONNAIRE; RNA SEQUENCE; SENSITIVITY ANALYSIS; STAPHYLOCOCCACEAE; ANIMAL; BIODIVERSITY; FAMILY SIZE; FECES; GENETICS; INTESTINE FLORA; MICROBIOLOGY; POULTRY; PRESCHOOL CHILD; RURAL POPULATION;

ANIMALS; BIODIVERSITY; CATTLE; CHICKENS; CHILD, PRESCHOOL; FAMILY CHARACTERISTICS; FECES; FEMALE; GASTROINTESTINAL MICROBIOME; HUMANS; KENYA; LIVESTOCK; MALE; POULTRY; RNA, RIBOSOMAL, 16S; RURAL POPULATION;

EID: 85011702165     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0171017     Document Type: Article

References (44)

1. Bendtsen KM, Fisker L, Hansen AK, Hansen CH, Nielsen DS. The influence of the young microbiome on inflammatory diseases-Lessons from animal studies. Birth defects research Part C, Embryo today: Reviews. 2015.
2. Althani A, Marei HE, Hamdi WS, Nasrallah GK, El Zowalaty ME, Al Khdor S, et al. Human Microbiome and Its Association With Health and Diseases. Journal of cellular physiology. 2015.
3. Nicholson JK, Holmes E, Kinross J, Burcelin R, Gibson G, Jia W, et al. Host-gut microbiota metabolic interactions. Science. 2012; 336(6086):1262-7. doi:10.1126/science.1223813 PMID: 22674330.
4. Hedin CR, McCarthy NE, Louis P, Farquharson FM, McCartney S, Taylor K, et al. Altered intestinal microbiota and blood T cell phenotype are shared by patients with Crohn's disease and their unaffected siblings. Gut. 2014.
5. Knip M, Siljander H. The role of the intestinal microbiota in type 1 diabetes mellitus. Nature reviews Endocrinology. 2016.
6. Zackular JP, Baxter NT, Iverson KD, Sadler WD, Petrosino JF, Chen GY, et al. The gut microbiome modulates colon tumorigenesis. MBio. 2013; 4(6):e00692-e13. doi:10.1128/mBio.00692-13 PMID: 24194538.
7. Gough EK, Stephens DA, Moodie EE, Prendergast AJ, Stoltzfus RJ, Humphrey JH, et al. Linear growth faltering in infants is associated with Acidaminococcus sp. and community-level changes in the gut microbiota. Microbiome. 2015; 3:24. doi:10.1186/s40168-015-0089-2 PMID: 26106478.
8. Ridaura VK, Faith JJ, Rey FE, Cheng J, Duncan AE, Kau AL, et al. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science. 2013; 341(6150):1241214. doi:10.1126/science.1241214 PMID: 24009397.
9. Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, Gordon JI. The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice Science Transitional Medicine [Internet]. 2009; 1(6).
10. Wu X, Ma C, Han L, Nawaz M, Gao F, Zhang X, et al. Molecular characterisation of the faecal microbiota in patients with type II diabetes. Current microbiology. 2010; 61(1):69-78. doi:10.1007/s00284-010-9582-9 PMID: 20087741.
11. Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J, Knight R, et al. Succession of microbial consortia in the developing infant gut microbiome. Proceedings of the National Academy of Sciences. 2011; 108(Supplement 1):4578-85.
12. Hollister EB, Riehle K, Luna RA, Weidler EM, Rubio-Gonzales M, Mistretta T-A, et al. Structure and function of the healthy pre-Adolescent pediatric gut microbiome. Microbiome. 2015; 3(1):1.
13. Sekirov I, Tam NM, Jogova M, Robertson ML, Li Y, Lupp C, et al. Antibiotic-induced perturbations of the intestinal microbiota alter host susceptibility to enteric infection. Infection and immunity. 2008; 76 (10):4726-36. doi:10.1128/IAI.00319-08 PMID: 18678663.
14. Faith JJ, Guruge JL, Charbonneau M, Subramanian S, Seedorf H, Goodman AL, et al. The long-Term stability of the human gut microbiota. Science. 2013; 341(6141):1237439. doi:10.1126/science.1237439 PMID: 23828941.
15. Tung J, Barreiro LB, Burns MB, Grenier JC, Lynch J, Grieneisen LE, et al. Social networks predict gut microbiome composition in wild baboons. Elife. 2015; 4.
16. Hospodsky D, Pickering AJ, Julian TR, Miller D, Gorthala S, Boehm AB, et al. Hand bacterial communities vary across two different human populations. Microbiology (Reading, England). 2014; 160(Pt6):1144-52.
17. Ruiz-Calderon JF, Cavallin H, Song SJ, Novoselac A, Pericchi LR, Hernandez JN, et al. Walls talk: Microbial biogeography of homes spanning urbanization. Sci Adv. 2016; 2(2):e1501061. doi:10.1126/sciadv.1501061 PMID: 26933683.
18. Moeller AH, Foerster S, Wilson ML, Pusey AE, Hahn BH, Ochman H. Social behavior shapes the chimpanzee pan-microbiome. Sci Adv. 2016; 2(1):e1500997. doi:10.1126/sciadv.1500997 PMID: 26824072.
19. Song SJ, Lauber C, Costello EK, Lozupone CA, Humphrey G, Berg-Lyons D, et al. Cohabiting Family Members Share Microbiota with One Another and with their Dogs. eLIFE. 2013; 2:1-22.
20. Azad MB, Konya T, Maughan H, Guttman DS, Field CJ, Sears MR, et al. Infant gut microbiota and the hygiene hypothesis of allergic disease: Impact of household pets and siblings on microbiota composition and diversity. Allergy, asthma, and clinical immunology: Official journal of the Canadian Society of Allergy and Clinical Immunology. 2013; 9(1):15.
21. Thumbi SM, Njenga MK, Marsh TL, Noh S, Otiang E, Munyua P, et al. Linking human health and livestock health: A "one-health" platform for integrated analysis of human health, livestock health, and economic welfare in livestock dependent communities. PloS one. 2015; 10(3):e0120761. doi:10.1371/journal.pone.0120761 PMID: 25798951.
22. Dai J, Gliniewicz K, Settles ML, Coats ER, McDonald AG. Influence of organic loading rate and solid retention time on polyhydroxybutyrate production from hybrid poplar hydrolysates using mixed microbial cultures. Bioresource technology. 2014; 175:23-33.
23. Probst M, Walde J, Pumpel T, Wagner AO, Schneider I, Insam H. Lactic acid fermentation within a cascading approach for biowaste treatment. Applied microbiology and biotechnology. 2015; 99(7):3029- 40. doi:10.1007/s00253-015-6414-7 PMID: 25652656.
24. Bokulich NA, Subramanian S, Faith JJ, Gevers D, Gordon JI, Knight R, et al. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods. 2013; 10(1):57-9. doi:10.1038/nmeth.2276 PMID: 23202435.
25. Westcott SL, Schloss PD. De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units. PeerJ. 2015; 3:e1487. doi:10.7717/peerj.1487 PMID: 26664811.
26. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic acids research. 2013; 41 (Database issue):D590-D6. doi:10.1093/nar/gks1219PMID: 23193283.
27. Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010; 26 (19):2460-1. doi:10.1093/bioinformatics/btq461 PMID: 20709691.
28. Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol. 2009; 26(7):1641-50. doi:10.1093/molbev/msp077PMID: 19377059.
29. Lozupone C, Knight R. UniFrac: A new phylogenetic method for comparing microbial communities. Applied Environmental Microbiology. 2005; 71(12):8228-35. doi:10.1128/AEM.71.12.8228-8235.2005 PMID: 16332807.
30. Anderson MJ, Crist TO, Chase JM, Vellend M, Inouye BD, Freestone AL, et al. Navigating the multiple meanings of beta diversity: A roadmap for the practicing ecologist. Ecol Lett. 2011; 14(1):19-28. doi:10.1111/j.1461-0248.2010.01552.xPMID: 21070562.
31. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-Throughput community sequencing data. Nat Methods. 2010; 7(5):335-6. doi:10.1038/nmeth.f.303 PMID: 20383131.
32. Mahe F, Rognes T, Quince C, de Vargas C, Dunthorn M. Swarm: Robust and fast clustering method for amplicon-based studies. PeerJ. 2014; 2:e593. doi:10.7717/peerj.593 PMID: 25276506.
33. Mahe F, Rognes T, Quince C, de Vargas C, Dunthorn M. Swarm v2: highly-scalable and high-resolution amplicon clustering. PeerJ. 2015; 3:e1420. doi:10.7717/peerj.1420 PMID: 26713226.
34. Lin A, Bik EM, Costello EK, Dethlefsen L, Haque R, Relman DA, et al. Distinct distal gut microbiome diversity and composition in healthy children from Bangladesh and the United States. PloS One. 2013; 8(1):e53838. doi:10.1371/journal.pone.0053838 PMID: 23349750.
35. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, et al. Human gut microbiome viewed across age and geography. Nature. 2012; 486(7402):222-7. doi:10.1038/nature11053PMID: 22699611.
36. Ellis RJ, Bruce KD, Jenkins C, Stothard JR, Ajarova L, Mugisha L, et al. Comparison of the Distal Gut Microbiota from People and Animals in Africa. PloS one. 2013; 8(1):1-11.
37. De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci U S A. 2010; 107(33):14691-6. doi:10.1073/pnas.1005963107 PMID: 20679230.
38. D'Argenio V, Salvatore F. The role of the gut microbiome in the healthy adult status. Clin Chim Acta. 2015; 451(Pt A):97-102. doi: 10.1016/j.cca.2015.01.003 PMID: 25584460.
39. Avershina E, Storro O, Oien T, Johnsen R, Pope P, Rudi K. Major faecal microbiota shifts in composition and diversity with age in a geographically restricted cohort of mothers and their children. FEMS Microbiol Ecol. 2014; 87(1):280-90. doi:10.1111/1574-6941.12223 PMID: 24112053.
40. Voreades N, Kozil A, Weir TL. Diet and the development of the human intestinal microbiome. Front Microbiol. 2014; 5:494. doi:10.3389/fmicb.2014.00494 PMID: 25295033.
41. Chong CW, Ahmad AF, Lim YA, Teh CS, Yap IK, Lee SC, et al. Effect of ethnicity and socioeconomic variation to the gut microbiota composition among pre-Adolescent in Malaysia. Sci Rep. 2015; 5:13338. doi:10.1038/srep13338 PMID: 26290472.
42. Ludvigsen J, Svihus B, Rudi K. Rearing Room Affects the Non-dominant Chicken Cecum Microbiota, While Diet Affects the Dominant Microbiota. Front Vet Sci. 2016; 3:16. doi:10.3389/fvets.2016.00016 PMID: 26942187.
43. Oakley BB, Kogut MH. Spatial and Temporal Changes in the Broiler Chicken Cecal and Fecal Microbiomes and Correlations of Bacterial Taxa with Cytokine Gene Expression. Front Vet Sci. 2016; 3:11. doi:10.3389/fvets.2016.00011 PMID: 26925404.
44. Dominianni C, Wu J, Hayes RB, Ahn J. Comparison of methods for fecal microbiome biospecimen collection. BMC Microbiol. 2014; 14:103. doi:10.1186/1471-2180-14-103 PMID: 24758293.