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1. Dental calculus and the evolution of the human oral microbiome

   Warinner, C (January 2016, Journal of the California Dental Association)

   Characterizing the evolution of the oral microbiome is a challenging, but increasingly feasible, task. Recently, dental calculus has been shown to preserve ancient biomolecules from the oral microbiota, host tissues and diet for tens of thousands of years. As such, it provides a unique window into the ancestral oral microbiome. This article reviews recent advancements in ancient dental calculus research and emerging insights into the evolution and ecology of the human oral microbiome. 

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2. Identification of the Bacterial Biosynthetic Gene Clusters of the Oral Microbiome Illuminates the Unexplored Social Language of Bacteria during Health and Disease

   https://doi.org/10.1128/mBio.00321-19  

   Aleti, Gajender; Baker, Jonathon L.; Tang, Xiaoyu; Alvarez, Ruth; Dinis, Márcia; Tran, Nini C.; Melnik, Alexey V.; Zhong, Cuncong; Ernst, Madeleine; Dorrestein, Pieter C.; et al (April 2019, mBio)

   ABSTRACT Small molecules are the primary communication media of the microbial world. Recent bioinformatic studies, exploring the biosynthetic gene clusters (BGCs) which produce many small molecules, have highlighted the incredible biochemical potential of the signaling molecules encoded by the human microbiome. Thus far, most research efforts have focused on understanding the social language of the gut microbiome, leaving crucial signaling molecules produced by oral bacteria and their connection to health versus disease in need of investigation. In this study, a total of 4,915 BGCs were identified across 461 genomes representing a broad taxonomic diversity of oral bacteria. Sequence similarity networking provided a putative product class for more than 100 unclassified novel BGCs. The newly identified BGCs were cross-referenced against 254 metagenomes and metatranscriptomes derived from individuals either with good oral health or with dental caries or periodontitis. This analysis revealed 2,473 BGCs, which were differentially represented across the oral microbiomes associated with health versus disease. Coabundance network analysis identified numerous inverse correlations between BGCs and specific oral taxa. These correlations were present in healthy individuals but greatly reduced in individuals with dental caries, which may suggest a defect in colonization resistance. Finally, corroborating mass spectrometry identified several compounds with homology to products of the predicted BGC classes. Together, these findings greatly expand the number of known biosynthetic pathways present in the oral microbiome and provide an atlas for experimental characterization of these abundant, yet poorly understood, molecules and socio-chemical relationships, which impact the development of caries and periodontitis, two of the world’s most common chronic diseases. IMPORTANCE The healthy oral microbiome is symbiotic with the human host, importantly providing colonization resistance against potential pathogens. Dental caries and periodontitis are two of the world’s most common and costly chronic infectious diseases and are caused by a localized dysbiosis of the oral microbiome. Bacterially produced small molecules, often encoded by BGCs, are the primary communication media of bacterial communities and play a crucial, yet largely unknown, role in the transition from health to dysbiosis. This study provides a comprehensive mapping of the BGC repertoire of the human oral microbiome and identifies major differences in health compared to disease. Furthermore, BGC representation and expression is linked to the abundance of particular oral bacterial taxa in health versus dental caries and periodontitis. Overall, this study provides a significant insight into the chemical communication network of the healthy oral microbiome and how it devolves in the case of two prominent diseases. 

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3. Integrating Satellite, UAV, and Ground-Based Remote Sensing in Archaeology: An Exploration of Pre-Modern Land Use in Northeastern Iraq

   https://doi.org/10.3390/rs13245119  

   Laugier, Elise Jakoby; Casana, Jesse (December 2021, Remote Sensing)

   Satellite remote sensing is well demonstrated to be a powerful tool for investigating ancient land use in Southwest Asia. However, few regional studies have systematically integrated satellite-based observations with more intensive remote sensing technologies, such as drone-deployed multispectral sensors and ground-based geophysics, to explore off-site areas. Here, we integrate remote sensing data from a variety of sources and scales including historic aerial photographs, modern satellite imagery, drone-deployed sensors, and ground-based geophysics to explore pre-modern land use along the Upper Diyala/Sirwan River in the Kurdistan Region of Iraq. Our analysis reveals an incredible diversity of land use features, including canals, qanats, trackways, and field systems, most of which likely date to the first millennium CE, and demonstrate the potential of more intensive remote sensing methods to resolve land use features. Our results align with broader trends across ancient Southwest Asia that document the most intensive land use in the first millennium BCE through the first millennium CE. Land use features dating to the earlier Bronze Age (fourth through second millennium BCE) remain elusive and will likely require other investigative approaches. 

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4. Oral metagenomes from Native American Ancestors reveal distinct microbial lineages in the pre‐contact era

   https://doi.org/10.1002/ajpa.24735  

   Honap, Tanvi P.; Monroe, Cara R.; Johnson, Sarah J.; Jacobson, David K.; Abin, Christopher A.; Austin, Rita M.; Sandberg, Paul; Levine, Marc; Sankaranarayanan, Krithivasan; Lewis, Jr., Cecil M. (April 2023, American Journal of Biological Anthropology)

   Abstract ObjectivesLimited studies have focused on how European contact and colonialism impacted Native American oral microbiomes, specifically, the diversity of commensal or opportunistically pathogenic oral microbes, which may be associated with oral diseases. Here, we studied the oral microbiomes of pre‐contact Wichita Ancestors, in partnership with the Descendant community, The Wichita and Affiliated Tribes, Oklahoma, USA. Materials and MethodsSkeletal remains of 28 Wichita Ancestors from 20 archeological sites (dating approximately to 1250–1450 CE) were paleopathologically assessed for presence of dental calculus and oral disease. DNA was extracted from calculus, and partial uracil deglycosylase‐treated double‐stranded DNA libraries were shotgun‐sequenced using Illumina technology. DNA preservation was assessed, the microbial community was taxonomically profiled, and phylogenomic analyzes were conducted. ResultsPaleopathological analysis revealed signs of oral diseases such as caries and periodontitis. Calculus samples from 26 Ancestors yielded oral microbiomes with minimal extraneous contamination. Anaerolineaceae bacterium oral taxon 439 was found to be the most abundant bacterial species. Several Ancestors showed high abundance of bacteria typically associated with periodontitis such asTannerella forsythiaandTreponema denticola. Phylogenomic analyzes of Anaerolineaceae bacterium oral taxon 439 andT. forsythiarevealed biogeographic structuring; strains present in the Wichita Ancestors clustered with strains from other pre‐contact Native Americans and were distinct from European and/or post‐contact American strains. DiscussionWe present the largest oral metagenome dataset from a pre‐contact Native American population and demonstrate the presence of distinct lineages of oral microbes specific to the pre‐contact Americas. 

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5. A Distinct Contractile Injection System Gene Cluster Found in a Majority of Healthy Adult Human Microbiomes

   https://doi.org/10.1128/mSystems.00648-20  

   Rojas, Maria I.; Cavalcanti, Giselle S.; McNair, Katelyn; Benler, Sean; Alker, Amanda T.; Cobián-Güemes, Ana G.; Giluso, Melissa; Levi, Kyle; Rohwer, Forest; Bailey, Barbara A.; et al (August 2020, mSystems)

   Gilbert, Jack A. (Ed.)

   ABSTRACT Many commensal bacteria antagonize each other or their host by producing syringe-like secretion systems called contractile injection systems (CIS). Members of the Bacteroidales family have been shown to produce only one type of CIS—a contact-dependent type 6 secretion system that mediates bacterium-bacterium interactions. Here, we show that a second distinct cluster of genes from Bacteroidales bacteria from the human microbiome may encode yet-uncharacterized injection systems that we term Bacteroidales injection systems (BIS). We found that BIS genes are present in the gut microbiomes of 99% of individuals from the United States and Europe and that BIS genes are more prevalent in the gut microbiomes of healthy individuals than in those individuals suffering from inflammatory bowel disease. Gene clusters similar to that of the BIS mediate interactions between bacteria and diverse eukaryotes, like amoeba, insects, and tubeworms. Our findings highlight the ubiquity of the BIS gene cluster in the human gut and emphasize the relevance of the gut microbiome to the human host. These results warrant investigations into the structure and function of the BIS and how they might mediate interactions between Bacteroidales bacteria and the human host or microbiome. IMPORTANCE To engage with host cells, diverse pathogenic bacteria produce syringe-like structures called contractile injection systems (CIS). CIS are evolutionarily related to the contractile tails of bacteriophages and are specialized to puncture membranes, often delivering effectors to target cells. Although CIS are key for pathogens to cause disease, paradoxically, similar injection systems have been identified within healthy human microbiome bacteria. Here, we show that gene clusters encoding a predicted CIS, which we term Bacteroidales injection systems (BIS), are present in the microbiomes of nearly all adult humans tested from Western countries. BIS genes are enriched within human gut microbiomes and are expressed both in vitro and in vivo . Further, a greater abundance of BIS genes is present within healthy gut microbiomes than in those humans with with inflammatory bowel disease (IBD). Our discovery provides a potentially distinct means by which our microbiome interacts with the human host or its microbiome. 

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