The Fruits of My Labor
Reconstruction of ancient microbial genomes from the human gut
Wibowo M., Yang Z., Borry M., Hubner A., Huang K., Tierney B., Zimmerman S., Barajas-Olmos F., Contreras-Cubas C., Garcia-Ortiz H., Martinez-Hernandez A., Luber J., Kirstahler P., Blohm T., Smiley F., Arnold R., Ballal S., Pamp S., Russ J., Maixner F., Rota-Stabelli O., Segata N., Reinhard K., Orozco L., Warinner C., Snow M., LeBlanc S., and Kostic A.
Nature, May 2021
Loss of gut microbial diversity1–6 in industrial populations is associated with chronic diseases7 , underscoring the importance of studying our ancestral gut microbiome. However, relatively little is known about the composition of pre-industrial gut microbiomes. Here we performed a large-scale de novo assembly of microbial genomes from palaeofaeces. From eight authenticated human palaeofaeces samples (1,000–2,000 years old) with well-preserved DNA from southwestern USA and Mexico, we reconstructed 498 medium- and high-quality microbial genomes. Among the 181 genomes with the strongest evidence of being ancient and of human gut origin, 39% represent previously undescribed species-level genome bins. Tip dating suggests an approximate diversifcation timeline for the key human symbiont Methanobrevibacter smithii. In comparison to 789 present-day human gut microbiome samples from eight countries, the palaeofaeces samples are more similar to non-industrialized than industrialized human gut microbiomes. Functional profling of the palaeofaeces samples reveals a markedly lower abundance of antibiotic-resistance and mucin-degrading genes, as well as enrichment of mobile genetic elements relative to industrial gut microbiomes. This study facilitates the discovery and characterization of previously undescribed gut microorganisms from ancient microbiomes and the investigation of the evolutionary history of the human gut microbiota through genome reconstruction from palaeofaeces.
UM Research Reveals Ancient People Had More Diverse Gut Microorganisms
Article published by the University of Montana due to the co-authorship of Dr. Meradeth Snow and myself on a prestigious Nature paper publication by Wibowo et al. (2021).
May 12, 2021
Marfa Public Radio Nature Notes: In Ancient DNA Findings, Profound Implications for Big Bend's Past, and Present
Schroeder, Blohm, and Snow were invited to discuss the recent findings from the Spirit Eye Cave (JAS:Reports, 2021) article on the Marfa Public Radio Nature Notes show which hosts various broadcasts on learning about the Big Bend area in West Texas.
February 11, 2021
Spirit Eye Cave: Reestablishing provenience of trafficked prehistoric human remains using a composite collection-based ancient DNA approach.
Byron Schroeder, Tre Blohm, Meradeth H. Snow, 2021
UM Earns Grant To Boost Research Network Infrastructure
September 11, 2020
UWO Senior Digs Fossils in Ukraine
November 9, 2017
Spirit Eye Cave, located on private land in west Texas near the US/Mexico border, contains as many as four human interments removed by pay-to-dig collectors in the 1950–60 s. The mitochondrial DNA results from two individuals indicate a maternal relationship between each interment. Considered together, these data indicate both a familiarity with the region and a stability of land use by foraging groups during a period of reputed instability. The identification of the B2a4a1 haplogroup in both individuals ties the region to indigenous groups in present-day Mexico, Texas, and the prehistoric site of Paquim´e, in Chihuahua, Mexico. These results demonstrate the utility of a collaborative collection based aDNA approach for looted and heavily collected sheltered sites.
An article published about new network and computer infrastructure upgrades at the University of Montana. I helped by providing project abstracts for the needs the Anthropology Department has with increasing computer infrastructure for aDNA analysis. Here is the link: UM Earns Grant to Boost Research Network Infrastructure (umt.edu)
I had an article published about my research in Ukraine by my undergraduate institutions newspaper organization, The Advance Titan. Here is the link: https://advancetitan.com/news/2017/11/09/uwo-senior-digs-fossils-ukraine