2021
Yates, James A. Fellows; Velsko, Irina M.; Aron, Franziska; Posth, Cosimo; Hofman, Courtney A.; Austin, Rita M.; Parker, Cody E.; Mann, Allison E.; Nägele, Kathrin; Arthur, Kathryn Weedman; Arthur, John W.; Bauer, Catherine C.; Crevecoeur, Isabelle; Cupillard, Christophe; Curtis, Matthew C.; Dalén, Love; Bonilla, Marta Díaz-Zorita; Fernández-Lomana, J. Carlos Díez; Drucker, Dorothée G.; Escrivá, Elena Escribano; Francken, Michael; Gibbon, Victoria E.; Morales, Manuel R. González; Mateu, Ana Grande; Harvati, Katerina; Henry, Amanda G.; Humphrey, Louise; Menéndez, Mario; Mihailović, Dušan; Peresani, Marco; Moroder, Sofía Rodríguez; Roksandic, Mirjana; Rougier, Hélène; Sázelová, Sandra; Stock, Jay T.; Straus, Lawrence Guy; Svoboda, Jiří; Teßmann, Barbara; Walker, Michael J.; Power, Robert C.; Lewis, Cecil M.; Sankaranarayanan, Krithivasan; Guschanski, Katerina; Wrangham, Richard W.; Dewhirst, Floyd E.; Salazar-García, Domingo C.; Krause, Johannes; Herbig, Alexander; Warinner, Christina
The evolution and changing ecology of the African hominid oral microbiome Journal Article
In: Proc Natl Acad Sci, vol. 118, no. 20, pp. e2021655118, 2021.
Abstract | Links | BibTeX | Tags: ancient DNA, bacteria, evolution, phylogenetics
@article{Yates:21,
title = {The evolution and changing ecology of the African hominid oral microbiome},
author = {James A. Fellows Yates and Irina M. Velsko and Franziska Aron and Cosimo Posth and Courtney A. Hofman and Rita M. Austin and Cody E. Parker and Allison E. Mann and Kathrin Nägele and Kathryn Weedman Arthur and John W. Arthur and Catherine C. Bauer and Isabelle Crevecoeur and Christophe Cupillard and Matthew C. Curtis and Love Dalén and Marta Díaz-Zorita Bonilla and J. Carlos Díez Fernández-Lomana and Dorothée G. Drucker and Elena Escribano Escrivá and Michael Francken and Victoria E. Gibbon and Manuel R. González Morales and Ana Grande Mateu and Katerina Harvati and Amanda G. Henry and Louise Humphrey and Mario Menéndez and Dušan Mihailović and Marco Peresani and Sofía Rodríguez Moroder and Mirjana Roksandic and Hélène Rougier and Sandra Sázelová and Jay T. Stock and Lawrence Guy Straus and Jiří Svoboda and Barbara Teßmann and Michael J. Walker and Robert C. Power and Cecil M. Lewis and Krithivasan Sankaranarayanan and Katerina Guschanski and Richard W. Wrangham and Floyd E. Dewhirst and Domingo C. Salazar-García and Johannes Krause and Alexander Herbig and Christina Warinner},
doi = {10.1073/pnas.2021655118},
year = {2021},
date = {2021-05-18},
urldate = {2021-05-18},
journal = {Proc Natl Acad Sci},
volume = {118},
number = {20},
pages = {e2021655118},
publisher = {Proceedings of the National Academy of Sciences},
abstract = {The oral microbiome plays key roles in human biology, health, and disease, but little is known about the global diversity, variation, or evolution of this microbial community. To better understand the evolution and changing ecology of the human oral microbiome, we analyzed 124 dental biofilm metagenomes from humans, including Neanderthals and Late Pleistocene to present-day modern humans, chimpanzees, and gorillas, as well as New World howler monkeys for comparison. We find that a core microbiome of primarily biofilm structural taxa has been maintained throughout African hominid evolution, and these microbial groups are also shared with howler monkeys, suggesting that they have been important oral members since before the catarrhine–platyrrhine split ca. 40 Mya. However, community structure and individual microbial phylogenies do not closely reflect host relationships, and the dental biofilms of Homo and chimpanzees are distinguished by major taxonomic and functional differences. Reconstructing oral metagenomes from up to 100 thousand years ago, we show that the microbial profiles of both Neanderthals and modern humans are highly similar, sharing functional adaptations in nutrient metabolism. These include an apparent Homo-specific acquisition of salivary amylase-binding capability by oral streptococci, suggesting microbial coadaptation with host diet. We additionally find evidence of shared genetic diversity in the oral bacteria of Neanderthal and Upper Paleolithic modern humans that is not observed in later modern human populations. Differences in the oral microbiomes of African hominids provide insights into human evolution, the ancestral state of the human microbiome, and a temporal framework for understanding microbial health and disease.},
keywords = {ancient DNA, bacteria, evolution, phylogenetics},
pubstate = {published},
tppubtype = {article}
}
The oral microbiome plays key roles in human biology, health, and disease, but little is known about the global diversity, variation, or evolution of this microbial community. To better understand the evolution and changing ecology of the human oral microbiome, we analyzed 124 dental biofilm metagenomes from humans, including Neanderthals and Late Pleistocene to present-day modern humans, chimpanzees, and gorillas, as well as New World howler monkeys for comparison. We find that a core microbiome of primarily biofilm structural taxa has been maintained throughout African hominid evolution, and these microbial groups are also shared with howler monkeys, suggesting that they have been important oral members since before the catarrhine–platyrrhine split ca. 40 Mya. However, community structure and individual microbial phylogenies do not closely reflect host relationships, and the dental biofilms of Homo and chimpanzees are distinguished by major taxonomic and functional differences. Reconstructing oral metagenomes from up to 100 thousand years ago, we show that the microbial profiles of both Neanderthals and modern humans are highly similar, sharing functional adaptations in nutrient metabolism. These include an apparent Homo-specific acquisition of salivary amylase-binding capability by oral streptococci, suggesting microbial coadaptation with host diet. We additionally find evidence of shared genetic diversity in the oral bacteria of Neanderthal and Upper Paleolithic modern humans that is not observed in later modern human populations. Differences in the oral microbiomes of African hominids provide insights into human evolution, the ancestral state of the human microbiome, and a temporal framework for understanding microbial health and disease.
2014
Schwartze, Volker U.; Winter, Sascha; Shelest, Ekaterina; Marcet-Houben, Marina; Horn, Fabian; Wehner, Stefanie; Linde, Jörg; Valiante, Vito; Sammeth, Michael; Riege, Konstantin; Nowrousian, Minou; Kaerger, Kerstin; Jacobsen, Ilse D.; Marz, Manja; Brakhage, Axel A.; Gabaldón, Toni; Böcker, Sebastian; Voigt, Kerstin
In: PLos Genet, vol. 10, pp. e1004496, 2014.
Abstract | Links | BibTeX | Tags: ancient DNA, assembly, evolution, fungi, RNA / transcriptomics, splicing
@article{Schwartze:14,
title = {Gene expansion shapes genome architecture in the human pathogen \textit{Lichtheimia corymbifera}: an evolutionary genomics analysis in the ancient terrestrial mucorales (Mucoromycotina)},
author = {Volker U. Schwartze and Sascha Winter and Ekaterina Shelest and Marina Marcet-Houben and Fabian Horn and Stefanie Wehner and Jörg Linde and Vito Valiante and Michael Sammeth and Konstantin Riege and Minou Nowrousian and Kerstin Kaerger and Ilse D. Jacobsen and Manja Marz and Axel A. Brakhage and Toni Gabaldón and Sebastian Böcker and Kerstin Voigt},
doi = {10.1371/journal.pgen.1004496},
year = {2014},
date = {2014-08-14},
urldate = {2014-08-14},
journal = {PLos Genet},
volume = {10},
pages = {e1004496},
abstract = {Lichtheimia species are the second most important cause of mucormycosis in Europe. To provide broader insights into the molecular basis of the pathogenicity-associated traits of the basal Mucorales, we report the full genome sequence of L. corymbifera and compared it to the genome of Rhizopus oryzae, the most common cause of mucormycosis worldwide. The genome assembly encompasses 33.6 MB and 12,379 protein-coding genes. This study reveals four major differences of the L. corymbifera genome to R. oryzae: (i) the presence of an highly elevated number of gene duplications which are unlike R. oryzae not due to whole genome duplication (WGD), (ii) despite the relatively high incidence of introns, alternative splicing (AS) is not frequently observed for the generation of paralogs and in response to stress, (iii) the content of repetitive elements is strikingly low (<5%), (iv) L. corymbifera is typically haploid. Novel virulence factors were identified which may be involved in the regulation of the adaptation to iron-limitation, e.g. LCor01340.1 encoding a putative siderophore transporter and LCor00410.1 involved in the siderophore metabolism. Genes encoding the transcription factors LCor08192.1 and LCor01236.1, which are similar to GATA type regulators and to calcineurin regulated CRZ1, respectively, indicating an involvement of the calcineurin pathway in the adaption to iron limitation. Genes encoding MADS-box transcription factors are elevated up to 11 copies compared to the 1-4 copies usually found in other fungi. More findings are: (i) lower content of tRNAs, but unique codons in L. corymbifera, (ii) Over 25% of the proteins are apparently specific for L. corymbifera. (iii) L. corymbifera contains only 2/3 of the proteases (known to be essential virulence factors) in comparison to R. oryzae. On the other hand, the number of secreted proteases, however, is roughly twice as high as in R. oryzae.},
keywords = {ancient DNA, assembly, evolution, fungi, RNA / transcriptomics, splicing},
pubstate = {published},
tppubtype = {article}
}
Lichtheimia species are the second most important cause of mucormycosis in Europe. To provide broader insights into the molecular basis of the pathogenicity-associated traits of the basal Mucorales, we report the full genome sequence of L. corymbifera and compared it to the genome of Rhizopus oryzae, the most common cause of mucormycosis worldwide. The genome assembly encompasses 33.6 MB and 12,379 protein-coding genes. This study reveals four major differences of the L. corymbifera genome to R. oryzae: (i) the presence of an highly elevated number of gene duplications which are unlike R. oryzae not due to whole genome duplication (WGD), (ii) despite the relatively high incidence of introns, alternative splicing (AS) is not frequently observed for the generation of paralogs and in response to stress, (iii) the content of repetitive elements is strikingly low (<5%), (iv) L. corymbifera is typically haploid. Novel virulence factors were identified which may be involved in the regulation of the adaptation to iron-limitation, e.g. LCor01340.1 encoding a putative siderophore transporter and LCor00410.1 involved in the siderophore metabolism. Genes encoding the transcription factors LCor08192.1 and LCor01236.1, which are similar to GATA type regulators and to calcineurin regulated CRZ1, respectively, indicating an involvement of the calcineurin pathway in the adaption to iron limitation. Genes encoding MADS-box transcription factors are elevated up to 11 copies compared to the 1-4 copies usually found in other fungi. More findings are: (i) lower content of tRNAs, but unique codons in L. corymbifera, (ii) Over 25% of the proteins are apparently specific for L. corymbifera. (iii) L. corymbifera contains only 2/3 of the proteases (known to be essential virulence factors) in comparison to R. oryzae. On the other hand, the number of secreted proteases, however, is roughly twice as high as in R. oryzae.