Tanvi P Honap

University of Oklahoma | ou · Department of Anthropology

Human microbiome studies are increasingly incorporating macroecological approaches, such as community assembly, network analysis and functional redundancy to more fully characterize the microbiome. Such analyses have not been applied to ancient human microbiomes, preventing insights into human microbiome evolution. We address this issue by analysin...

CrAssphage (cross-assembly phage) is a bacteriophage that was first discovered in human gut metagenomic data. CrAssphage belongs to a diverse family of crAss-like bacteriophages thought to infect gut commensal bacteria belonging to Bacteroides species. However, not much is known about the biogeography of crAssphage and whether certain strains are a...

Leprosy is caused by the bacterial pathogens Mycobacterium leprae and Mycobacterium lepromatosis. Apart from humans, animals such as nine-banded armadillos in the Americas and red squirrels in the British Isles are naturally infected with M. leprae. Natural leprosy has also been reported in certain nonhuman primates, but it is not known whether the...

Mycobacterium lepraemurium is the causative agent of murine leprosy, a chronic, granulomatous disease similar to human leprosy. Due to the similar clinical manifestations of human and murine leprosy and the difficulty of growing both bacilli axenically, Mycobacterium leprae and M. lepraemurium were once thought to be closely related, although it wa...

Vitamin D is known to affect pathogenesis of dengue through modulation of immune responses. Vitamin D exerts its effects through vitamin D receptor (VDR). The functioning of VDR is affected by the gene polymorphisms in the coding (rs2228570) and 3'untranslated region (UTR) (rs1544410, rs7975232 and rs731236). In the present study, VDR gene polymorp...

Previous ancient DNA research has shown that Mycobacterium pinnipedii, which today causes tuberculosis (TB) primarily in pinnipeds, infected human populations living in the coastal areas of Peru prior to European colonization. Skeletal evidence indicates the presence of TB in several pre-colonial South and North American populations with minimal ac...

Many studies investigating the human microbiome-cancer interface have focused on the gut microbiome and gastrointestinal cancers. Outside of human papillomavirus driving cervical cancer, little is known about the relationship between the vaginal microbiome and other gynecological cancers, such as ovarian cancer. In this retrospective study, we inve...

Paragraph Among the biomolecules at the center of human health and molecular biology is a system of molecules that defines the human phenotype known as the metabolome. Through an untargeted metabolomic analysis of fecal samples from human individuals from Africa and the Americas—the birthplace and the last continental expansion of our species, resp...

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

High taxonomic diversity in non-industrial human gut microbiomes is often interpreted as beneficial; however, it is unclear if taxonomic diversity engenders ecological resilience (i.e. community stability and metabolic continuity). We estimate resilience through genus and species-level richness, phylogenetic diversity, and evenness in short-chain f...

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 micros...

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 micros...

Background: Termites are an important food resource for many human populations around the world, and are a good supply of nutrients. The fungus-farming 'higher' termite members of Macrotermitinae are also consumed by modern great apes and are implicated as critical dietary resources for early hominins. While the chemical nutritional composition of...

CrAssphage (cross-assembly phage) is a bacteriophage that was first discovered in human gut metagenomic data. CrAssphage belongs to a diverse family of crAss-like bacteriophages thought to infect gut commensal bacteria belonging to Bacteroides species. However, not much is known about the biogeography of crAssphage and whether certain strains are a...

Maximum parsimony tree of M. leprae strains. M. lepromatosis was used as an outgroup to root the tree (branch truncated for clarity). Bootstrap support estimated from 1,000 replicates is given next to each internal branch. The five M. leprae branches are highlighted. The nonhuman primate M. leprae genomes sequenced in this study are marked in red....

Case details of the three nonhuman primates with leprosy included in this study. (XLSX)

List of positions in the M. leprae reference genome excluded from phylogenetic analyses. (TXT)

Map showing the geographic ranges of chimpanzees (Red) and sooty mangabeys (Blue) in Africa. The overlap between the two species’ ranges is shown in purple. The map was generated using RStudio. (TIFF)

Summary of SNPs found in the nonhuman primate M. leprae strains. (XLSX)

Neighbor joining tree of M. leprae strains. M. lepromatosis was used as an outgroup to root the tree (branch truncated for clarity). Bootstrap support estimated from 1,000 replicates is given next to each internal branch. The five M. leprae branches are highlighted. The nonhuman primate M. leprae genomes sequenced in this study are denoted in red....

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Objectives: Archaeological dental calculus is a rich source of host-associated biomolecules. Importantly, however, dental calculus is more accurately described as a calcified microbial biofilm than a host tissue. As such, concerns regarding destructive analysis of human remains may not apply as strongly to dental calculus, opening the possibility...

In recent years, dental calculus has emerged as an important source of ancient genetic material. However, calculus has not been extensively utilized as a source of endogenous host DNA when working with human skeletal remains. In this study we compare endogenous DNA yields obtained from extractions performed from both dental calculus and dental toot...

The majority of emerging or reemerging infectious diseases are zoonoses. For example, tuberculosis, which is caused by members of the Mycobacterium tuberculosis complex (MTBC), shows bidirectional transmission among humans and several other mammalian species including nonhuman primates. M. leprae causes leprosy, primarily affecting humans and nine...

Oligoadenylate synthetases (OAS) play an important role in the immune response against dengue virus. Single nucleotide polymorphisms (SNPs) in the OAS genes are known to affect OAS activity and are associated with outcome of viral infections. Polymorphisms in the OAS1 (rs1131454 and rs10774671), OAS3 (rs2285932 and rs2072136) and OAS2 (rs15895 and...