publication . Article . Other literature type . Preprint . 2020

Multi-proxy analyses of a mid-15th century Middle Iron Age Bantu-speaker palaeo-faecal specimen elucidates the configuration of the 'ancestral' sub-Saharan African intestinal microbiome.

Anders J. Hansen; Tina B. Brand; Grant Hall; Eske Willerslev; Eske Willerslev; Eske Willerslev; Stephan Woodborne; Marnie Potgieter; Yves Van de Peer; Yves Van de Peer; ...
Open Access English
  • Published: 06 May 2020 Journal: Microbiome (issn: 2049-2618, Copyright policy)
  • Publisher: BMC
Abstract
Funder: Ministère des Affaires Etrangères; doi: http://dx.doi.org/10.13039/501100003763 Abstract: Background: The archaeological incidence of ancient human faecal material provides a rare opportunity to explore the taxonomic composition and metabolic capacity of the ancestral human intestinal microbiome (IM). Here, we report the results of the shotgun metagenomic analyses of an ancient South African palaeo-faecal specimen. Methods: Following the recovery of a single desiccated palaeo-faecal specimen from Bushman Rock Shelter in Limpopo Province, South Africa, we applied a multi-proxy analytical protocol to the sample. The extraction of ancient DNA from the speci...
Subjects
free text keywords: Ancient DNA, Human evolution, Molecular ecology, Intestinal microbiome, Taxonomic composition, Metabolic capacity, Microbial ecology, QR100-130, Research, Biology and Life Sciences, CHAIN CHLORINATED PARAFFINS [KeyWords Plus], GUT MICROBIOTA, DNA, PATTERNS, DAMAGE, IMPACT, ENTEROTYPES, RESISTANCE, DIVERSITY, DYSBIOSIS, [SHS]Humanities and Social Sciences, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, /dk/atira/pure/researchoutput/pubmedpublicationtype/D016428, Journal Article, /dk/atira/pure/researchoutput/pubmedpublicationtype/D013485, Research Support, Non-U.S. Gov't, Enterotype, Biology, Iceman, Bantu languages, Metagenomics, Zoology, Rock shelter, Ecology, Multi proxy, Geography, Sub saharan
Funded by
WT
Project
  • Funder: Wellcome Trust (WT)
112 references, page 1 of 8

1. J. Lederberg, A. T. McCray, 'Ome sweet' omics: A genealogical treasury of words. Scientist 15, 8 (2010).

2. C. Warinner, C. Speller, M. J. Collins, C. M. Lewis, Ancient human microbiomes. J Hum Evol. 79, 125-136 (2015). [OpenAIRE]

3. E. Thursby, N. Juge, Introduction to the human gut microbiota. Biochem J. 474, 1823-1836 (2017). [OpenAIRE]

4. L. W. van den Elsen, H. C. Poyntz, L. S. Weyrich, W. Young, E. E. Forbes-Blom, Embracing the gut microbiota: The new frontier for inflammatory and infectious diseases. Clin Transl Immunology 6, doi: 10.1038/cti.2016.91 (2017).

5. J. C. Clemente. E. C. Pehrsson, M. J. Blaser, K. Sandhu, Z. Gao, B. Wang, M. Magris, G. Hidalgo, M Contreras, Ó. Noya-Alarcón, O. Lander, J. McDonald, M. Cox, J. Walter, P. L. Oh, J. F. Ruiz, S. Rodriguez, N. Shen, S. J. Song, J. Metcalf, R. Knight, G. Dantas, M. G. Dominguez-Bello, The microbiome of uncontacted Amerindians. Sci Adv. 1, doi: 10.1126/sciadv.1500183 (2015).

6. E. R. Davenport, J. G. Sanders, S. J. Song, K. R. Amato, A. G. Clark, R. Knight, The human microbiome in evolution. BMC Biol. 15, doi: 10.1186/s12915-017-0454-7 (2017).

7. M. J. Blaser, The past and future biology of the human microbiome in an age of extinctions. Cell 172, 1173-1177 (2018). [OpenAIRE]

8. S. L. Schnorr, M. Candela, S. Rampelli, M. Centanni, C. Consolandi, G. Basaglia, S. Turroni, E. Biagi, C. Peano, M. Severgnini, J. Fiori, R. Gotti, G. De Bellis, D. Luiselli, P. Brigidi, A. Mabulla, F. Marlowe, A. G. Henry, A. N. Crittenden, Gut microbiome of the Hadza hunter-gatherers. Nat Commun. 5, doi: 10.1038/ncomms4654 (2014).

9. A. J. Obregon-Tito, R. Y. Tito, J. Metcalf, K. Sankaranarayanan, J. C. Clemente, L. K. Ursell, Z. Zech Xu, W. Van Treuren, R. Knight, P. M. Gaffney, P. Spicer, P. Lawson, L. Marin-Reyes, O. Trujillo-Villarroel, M. Foster, E. Guija-Poma, L. Troncoso-Corzo, C. Warinner, A. T. Ozga, C. M. Lewis, Subsistence strategies in traditional societies distinguish gut microbiomes. Nat Commun. 6505, doi: 10.1038/ncomms7505 (2015).

10. C. Warinner, C. M. Lewis, Microbiome and health in past and present human populations. Am Anthrop. 117, 740-741 (2015). [OpenAIRE]

11. R. Lee, R. H. Daly, Cambridge encyclopaedia of hunters and gatherers. Cambridge, Cambridge University Press ISBN 9780521609197 (1999).

12. A. Gomez, K. J. Petrzelkova, M. B. Burns, C. J. Yeoman, A. R. Amato, K. Vlckova, D. Modry, A. Todd, C. A. Jost Robinson, M. J. Remis, M. G. Torralba, E. Morton, J. D. Umaña, F. Carbonero, H. R. Gaskins, K. E. Nelson, B. A. Wilson, R. M. Stumpf, B. A. White, S. R. Leigh, Gut microbiome of coexisting BaAka Pygmies and Bantu reflects gradients of traditional subsistence patterns. Cell Rep. 14, 2142-2153 (2016).

13. C. Girard, N. Tromas, M. Amyot, B. J. Shapiro, Gut microbiome of the Canadian Arctic Inuit. mSphere 2, doi: 10.1128/mSphere.00297-16 (2017).

14. A. Y. Voigt, P. I. Costea, J. R. Kultima, S. S. Li, G. Zeller, S. Sunagawa, P. Bork, Temporal and technical variability of human gut metagenomes. Genome Biol. 16, doi: 10.1186/s13059-015-0639-8 (2015).

15. J. Walter, R. Ley, The human gut microbiome: Ecology and recent evolutionary changes. Annu Rev Microbiol. 65, 411-429 (2011).

112 references, page 1 of 8
Abstract
Funder: Ministère des Affaires Etrangères; doi: http://dx.doi.org/10.13039/501100003763 Abstract: Background: The archaeological incidence of ancient human faecal material provides a rare opportunity to explore the taxonomic composition and metabolic capacity of the ancestral human intestinal microbiome (IM). Here, we report the results of the shotgun metagenomic analyses of an ancient South African palaeo-faecal specimen. Methods: Following the recovery of a single desiccated palaeo-faecal specimen from Bushman Rock Shelter in Limpopo Province, South Africa, we applied a multi-proxy analytical protocol to the sample. The extraction of ancient DNA from the speci...
Subjects
free text keywords: Ancient DNA, Human evolution, Molecular ecology, Intestinal microbiome, Taxonomic composition, Metabolic capacity, Microbial ecology, QR100-130, Research, Biology and Life Sciences, CHAIN CHLORINATED PARAFFINS [KeyWords Plus], GUT MICROBIOTA, DNA, PATTERNS, DAMAGE, IMPACT, ENTEROTYPES, RESISTANCE, DIVERSITY, DYSBIOSIS, [SHS]Humanities and Social Sciences, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, /dk/atira/pure/researchoutput/pubmedpublicationtype/D016428, Journal Article, /dk/atira/pure/researchoutput/pubmedpublicationtype/D013485, Research Support, Non-U.S. Gov't, Enterotype, Biology, Iceman, Bantu languages, Metagenomics, Zoology, Rock shelter, Ecology, Multi proxy, Geography, Sub saharan
Funded by
WT
Project
  • Funder: Wellcome Trust (WT)
112 references, page 1 of 8

1. J. Lederberg, A. T. McCray, 'Ome sweet' omics: A genealogical treasury of words. Scientist 15, 8 (2010).

2. C. Warinner, C. Speller, M. J. Collins, C. M. Lewis, Ancient human microbiomes. J Hum Evol. 79, 125-136 (2015). [OpenAIRE]

3. E. Thursby, N. Juge, Introduction to the human gut microbiota. Biochem J. 474, 1823-1836 (2017). [OpenAIRE]

4. L. W. van den Elsen, H. C. Poyntz, L. S. Weyrich, W. Young, E. E. Forbes-Blom, Embracing the gut microbiota: The new frontier for inflammatory and infectious diseases. Clin Transl Immunology 6, doi: 10.1038/cti.2016.91 (2017).

5. J. C. Clemente. E. C. Pehrsson, M. J. Blaser, K. Sandhu, Z. Gao, B. Wang, M. Magris, G. Hidalgo, M Contreras, Ó. Noya-Alarcón, O. Lander, J. McDonald, M. Cox, J. Walter, P. L. Oh, J. F. Ruiz, S. Rodriguez, N. Shen, S. J. Song, J. Metcalf, R. Knight, G. Dantas, M. G. Dominguez-Bello, The microbiome of uncontacted Amerindians. Sci Adv. 1, doi: 10.1126/sciadv.1500183 (2015).

6. E. R. Davenport, J. G. Sanders, S. J. Song, K. R. Amato, A. G. Clark, R. Knight, The human microbiome in evolution. BMC Biol. 15, doi: 10.1186/s12915-017-0454-7 (2017).

7. M. J. Blaser, The past and future biology of the human microbiome in an age of extinctions. Cell 172, 1173-1177 (2018). [OpenAIRE]

8. S. L. Schnorr, M. Candela, S. Rampelli, M. Centanni, C. Consolandi, G. Basaglia, S. Turroni, E. Biagi, C. Peano, M. Severgnini, J. Fiori, R. Gotti, G. De Bellis, D. Luiselli, P. Brigidi, A. Mabulla, F. Marlowe, A. G. Henry, A. N. Crittenden, Gut microbiome of the Hadza hunter-gatherers. Nat Commun. 5, doi: 10.1038/ncomms4654 (2014).

9. A. J. Obregon-Tito, R. Y. Tito, J. Metcalf, K. Sankaranarayanan, J. C. Clemente, L. K. Ursell, Z. Zech Xu, W. Van Treuren, R. Knight, P. M. Gaffney, P. Spicer, P. Lawson, L. Marin-Reyes, O. Trujillo-Villarroel, M. Foster, E. Guija-Poma, L. Troncoso-Corzo, C. Warinner, A. T. Ozga, C. M. Lewis, Subsistence strategies in traditional societies distinguish gut microbiomes. Nat Commun. 6505, doi: 10.1038/ncomms7505 (2015).

10. C. Warinner, C. M. Lewis, Microbiome and health in past and present human populations. Am Anthrop. 117, 740-741 (2015). [OpenAIRE]

11. R. Lee, R. H. Daly, Cambridge encyclopaedia of hunters and gatherers. Cambridge, Cambridge University Press ISBN 9780521609197 (1999).

12. A. Gomez, K. J. Petrzelkova, M. B. Burns, C. J. Yeoman, A. R. Amato, K. Vlckova, D. Modry, A. Todd, C. A. Jost Robinson, M. J. Remis, M. G. Torralba, E. Morton, J. D. Umaña, F. Carbonero, H. R. Gaskins, K. E. Nelson, B. A. Wilson, R. M. Stumpf, B. A. White, S. R. Leigh, Gut microbiome of coexisting BaAka Pygmies and Bantu reflects gradients of traditional subsistence patterns. Cell Rep. 14, 2142-2153 (2016).

13. C. Girard, N. Tromas, M. Amyot, B. J. Shapiro, Gut microbiome of the Canadian Arctic Inuit. mSphere 2, doi: 10.1128/mSphere.00297-16 (2017).

14. A. Y. Voigt, P. I. Costea, J. R. Kultima, S. S. Li, G. Zeller, S. Sunagawa, P. Bork, Temporal and technical variability of human gut metagenomes. Genome Biol. 16, doi: 10.1186/s13059-015-0639-8 (2015).

15. J. Walter, R. Ley, The human gut microbiome: Ecology and recent evolutionary changes. Annu Rev Microbiol. 65, 411-429 (2011).

112 references, page 1 of 8
Any information missing or wrong?Report an Issue