CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content

被引：29

作者：

Borry, Maxime ^{[1
]}

Cordova, Bryan ^{[1
]}

Perri, Angela ^{[2
,3
]}

Wibowo, Marsha ^{[4
,5
,6
]}

Honap, Tanvi Prasad ^{[7
,8
]}

Ko, Jada ^{[9
]}

Yu, Jie ^{[10
]}

Britton, Kate ^{[3
,11
]}

Girdland-Flink, Linus ^{[11
,12
]}

Power, Robert C. ^{[3
,13
]}

Stuijts, Ingelise ^{[14
]}

Salazar-Garcia, Domingo C. ^{[15
,16
]}

Hofman, Courtney ^{[7
,8
]}

Hagan, Richard ^{[1
]}

Kagone, Therese Samdapawinde ^{[17
]}

Meda, Nicolas ^{[17
]}

Carabin, Helene ^{[18
]}

Jacobson, David ^{[7
,8
]}

Reinhard, Karl ^{[19
]}

Lewis, Cecil ^{[7
,8
]}

Kostic, Aleksandar ^{[4
,5
,6
]}

Jeong, Choongwon ^{[1
,20
]}

Herbig, Alexander ^{[1
]}

Huebner, Alexander ^{[1
]}

Warinner, Christina ^{[1
,9
,21
]}

机构：

[1] Max Planck Inst Sci Human Hist, Dept Archaeogenet, Jena, Germany

[2] Univ Durham, Dept Archaeol, Durham, England

[3] Max Planck Inst Evolutionary Anthropol, Dept Human Evolut, Leipzig, Germany

[4] Joslin Diabet Ctr, Sect Pathophysiol & Mol Pharmacol, Boston, MA 02215 USA

[5] Joslin Diabet Ctr, Sect Islet Cell & Regenerat Biol, Boston, MA 02215 USA

[6] Harvard Med Sch, Dept Microbiol, Boston, MA 02115 USA

[7] Univ Oklahoma, Dept Anthropol, Norman, OK 73019 USA

[8] Univ Oklahoma, LMAMR, Norman, OK 73019 USA

[9] Harvard Univ, Dept Anthropol, Cambridge, MA 02138 USA

[10] Wuhan Univ, Dept Hist, Wuhan, Peoples R China

[11] Univ Aberdeen, Dept Archaeol, Aberdeen, Scotland

[12] Liverpool John Moores Univ, Sch Nat Sci & Psychol, Liverpool, Merseyside, England

[13] Ludwig Maximilians Univ Munchen, Inst Vor & Fruhgeschichtl Archaol & Prov Rom Arch, Munich, Germany

[14] Discovery Programme, Dublin, Ireland

[15] IKERBASQUE Basque Fdn Sci, Grp Invest Prehist IT 1223 19, UPV EHU, Vitoria, Spain

[16] Univ Valencia, Dept Prehist Arqueol & Hist Antiga, Valencia, Spain

[17] Ctr Muraz, Bobo Dioulasso, Burkina Faso

[18] Univ Montreal, Fac Med Vet, Dept Pathol & Microbiol, St Hyacinthe, PQ, Canada

[19] Univ Nebraska, Sch Nat Resources, Lincoln, NE USA

[20] Seoul Natl Univ, Sch Biol Sci, Seoul, South Korea

[21] Friedrich Schiller Univ Jena, Fac Biol Sci, Jena, Germany

来源：

PEERJ | 2020年 / 8卷

基金：

美国国家卫生研究院;

关键词：

Coprolite; Paleofeces; Microbiome; Endogenous DNA; Archeology; Machine learning; Nextflow; Gut; Human; Dog; MOLECULAR ANALYSIS; ANCIENT DNA; DIET; DOGS; DIVERSITY; CULTURE; GENOME;

D O I：

10.7717/peerj.9001

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Shotgun metagenomics applied to archaeological feces (paleofeces) can bring new insights into the composition and functions of human and animal gut microbiota from the past. However, paleofeces often undergo physical distortions in archaeological sediments, making their source species difficult to identify on the basis of fecal morphology or microscopic features alone. Here we present a reproducible and scalable pipeline using both host and microbial DNA to infer the host source of fecal material. We apply this pipeline to newly sequenced archaeological specimens and show that we are able to distinguish morphologically similar human and canine paleofeces, as well as non-fecal sediments, from a range of archaeological contexts.

引用

页数：23

共 56 条

[31] Year-Round Shotgun Metagenomes Reveal Stable Microbial Communities in Agricultural Soils and Novel Ammonia Oxidizers Responding to Fertilization [J].

Orellana, Luis H. ;

Chee-Sanford, Joanne C. ;

Sanford, Robert A. ;

Loffler, Frank E. ;

Konstantinidis, Konstantinos T. .

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2018, 84 (02)

[32] Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle [J].

Pasolli, Edoardo ;

Asnicar, Francesco ;

Manara, Serena ;

Zolfo, Moreno ;

Karcher, Nicolai ;

Armanini, Federica ;

Beghini, Francesco ;

Manghi, Paolo ;

Tett, Adrian ;

Ghensi, Paolo ;

Carmen Collado, Maria ;

Rice, Benjamin L. ;

DuLong, Casey ;

Morgan, Xochitl C. ;

Golden, Christopher D. ;

Quince, Christopher ;

Huttenhower, Curtis ;

Segata, Nicola .

CELL, 2019, 176 (03) :649-+

[33] Good to Pet and Eat: The Keeping and Consuming of Dogs and Cats in South Korea [J].

Podberscek, Anthony L. .

JOURNAL OF SOCIAL ISSUES, 2009, 65 (03) :615-632

[34]

Poinar H, 2009, SCIENCE, V325, DOI 10.1126/science.1168182

[35] Molecular coproscopy:: Dung and diet of the extinct ground sloth Nothrotheriops shastensis [J].

Poinar, HN ;

Hofreiter, M ;

Spaulding, WG ;

Martin, PS ;

Stankiewicz, BA ;

Bland, H ;

Evershed, RP ;

Possnert, G ;

Pääbo, S .

SCIENCE, 1998, 281 (5375) :402-406

[36] A molecular analysis of dietary diversity for three archaic Native Americans [J].

Poinar, HN ;

Kuch, M ;

Sobolik, KD ;

Barnes, I ;

Stankiewicz, AB ;

Kuder, T ;

Spaulding, WG ;

Bryant, VM ;

Cooper, A ;

Pääbo, S .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2001, 98 (08) :4317-4322

[37]

Pysam Developers, 2018, PYS PYTH MOD READ MA

[38] Metagenome Sequencing of the Hadza Hunter-Gatherer Gut Microbiota [J].

Rampelli, Simone ;

Schnorr, Stephanie L. ;

Consolandi, Clarissa ;

Turroni, Silvia ;

Severgnini, Marco ;

Peano, Clelia ;

Brigidi, Patrizia ;

Crittenden, Alyssa N. ;

Henry, Amanda G. ;

Candela, Marco .

CURRENT BIOLOGY, 2015, 25 (13) :1682-1693

[39]

Reinhard K.J., 1992, Papers in Natural Resources, P245

[40] Partial uracil - DNA - glycosylase treatment for screening of ancient DNA [J].

Rohland, Nadin ;

Harney, Eadaoin ;

Mallick, Swapan ;

Nordenfelt, Susanne ;

Reich, David .

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 2015, 370 (1660)

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