Human gut microbiome viewed across age and geography
Tanya Yatsunenko,Federico E. Rey,Mark J. Manary,Mark J. Manary,Indi Trehan,Indi Trehan,Maria Gloria Dominguez-Bello,Monica Contreras,Magda Magris,Glida Hidalgo,Robert N. Baldassano,Andrey P. Anokhin,Andrew C. Heath,Barbara B. Warner,Jens Reeder,Justin Kuczynski,J. Gregory Caporaso,Catherine A. Lozupone,Christian L. Lauber,Jose C. Clemente,Dan Knights,Rob Knight,Jeffrey I. Gordon +22 more
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TLDR
The need to consider the microbiome when evaluating human development, nutritional needs, physiological variations and the impact of westernization is underscored, as distinctive features of the functional maturation of the gut microbiome are evident in early infancy as well as adulthood.Abstract:
Gut microbial communities represent one source of human genetic and metabolic diversity. To examine how gut microbiomes differ among human populations, here we characterize bacterial species in fecal samples from 531 individuals, plus the gene content of 110 of them. The cohort encompassed healthy children and adults from the Amazonas of Venezuela, rural Malawi and US metropolitan areas and included mono- and dizygotic twins. Shared features of the functional maturation of the gut microbiome were identified during the first three years of life in all three populations, including age-associated changes in the genes involved in vitamin biosynthesis and metabolism. Pronounced differences in bacterial assemblages and functional gene repertoires were noted between US residents and those in the other two countries. These distinctive features are evident in early infancy as well as adulthood. Our findings underscore the need to consider the microbiome when evaluating human development, nutritional needs, physiological variations and the impact of westernization.read more
Citations
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Developmental origins of nonalcoholic fatty liver disease
TL;DR: Human studies using magnetic resonance imaging have shown that maternal BMI predicts infant intrahepatocellular lipid storage, as seen in animal models, and the generational transfer of NAFLD may occur via epigenetic changes in offspring liver.
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Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification
Kirsten A. Ziesemer,Allison E. Mann,Krithivasan Sankaranarayanan,Hannes Schroeder,Hannes Schroeder,Andrew T. Ozga,Bernd W. Brandt,Egija Zaura,Andrea L. Waters-Rist,Menno L. P. Hoogland,Domingo C. Salazar-García,Mark Aldenderfer,Camilla Speller,Jessica Hendy,Darlene A. Weston,Darlene A. Weston,Sandy J. Macdonald,Gavin H. Thomas,Matthew J. Collins,Cecil M. Lewis,Corinne L. Hofman,Christina Warinner +21 more
TL;DR: It is concluded that systematic amplification bias confounds attempts to accurately reconstruct microbiome taxonomic profiles from 16S rRNA V3 amplicon data generated using universal primers, and advocate for the use of a shotgun metagenomics approach in ancient microbiome reconstructions.
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The subgingival periodontal microbiota of the aging mouth
TL;DR: An overview of the composition of the subgingival biofilm in older adults and the potential effects of age on the oral microbiome is provided and the relationship of the aging oral microbiota and Alzheimer's disease is examined.
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Biological control in the microbiome era: Challenges and opportunities
TL;DR: The five main challenges of microbiome implementation in biocontrol research are described, i.e. the management of technical errors and biases, the growing importance of bioinformatics, the adaptation of experimental schemes, the appropriate interplay between NGS and other technologies, and the need to complete current genome databases.
Journal ArticleDOI
Elevated rates of horizontal gene transfer in the industrialized human microbiome.
Mathieu Groussin,Mathilde Poyet,Ainara Sistiaga,Ainara Sistiaga,Sean M. Kearney,Katya Moniz,Mary Noel,Mary Noel,Jeff Hooker,Jeff Hooker,Sean M. Gibbons,Sean M. Gibbons,Sean M. Gibbons,Laure Ségurel,Laure Ségurel,Alain Froment,Alain Froment,Rihlat Said Mohamed,Alain Fezeu,Alain Fezeu,Vanessa A. Juimo,Vanessa A. Juimo,Sophie Lafosse,Francis Ekwin Tabe,Catherine Girard,Catherine Girard,Catherine Girard,Deborah Iqaluk,Le Thanh Tu Nguyen,B. Jesse Shapiro,Jenni Lehtimäki,Jenni Lehtimäki,Jenni Lehtimäki,Lasse Ruokolainen,Lasse Ruokolainen,Pinja P. Kettunen,Pinja P. Kettunen,Tommi Vatanen,Tommi Vatanen,Tommi Vatanen,Shani Sigwazi,Shani Sigwazi,Audax Mabulla,Audax Mabulla,Manuel Domínguez-Rodrigo,Manuel Domínguez-Rodrigo,Yvonne Ayerki Nartey,Yvonne Ayerki Nartey,Adwoa Agyei-Nkansah,Adwoa Agyei-Nkansah,Amoako Duah,Yaw Asante Awuku,Yaw Asante Awuku,Kenneth Valles,Kenneth Valles,Shadrack O. Asibey,Shadrack O. Asibey,Mary Afihene,Mary Afihene,Lewis R. Roberts,Lewis R. Roberts,Amelie Plymoth,Amelie Plymoth,Charles A Onyekwere,Charles A Onyekwere,Roger E. Summons,Ramnik J. Xavier,Eric J. Alm +67 more
TL;DR: This paper investigated the extent to which the rates and targets of horizontal gene transfer vary across thousands of bacterial strains from 15 human populations spanning a range of industrialization and found that industrialized lifestyles are associated with higher HGT rates and the functions of HGTs are related to the level of host industrialization.
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QIIME allows analysis of high-throughput community sequencing data.
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