The primary focus of archaeology has historically centered around humans, and their actions and impacts on this earth. However, the focus of this book has revolved around understanding the multispecies interactions that have occurred throughout time. Intriguingly, many of the impacts and alterations from human life and adaptation have gone unseen, and remains largely unexamined to this day. Microorganisms coat every surface of the earth – the ground we walk on, the air we breathe, the bodies we live in, the water we drink, and the animals and artifacts we interact with on a daily basis. Every decision, movement, and interaction that humans have with the earth impacts these microorganisms. Therefore, it has become critical to examine these diverse microbial communities in the world, and examine how human activity altered and impacted these inter-species relationships. While a unique form of multispecies interaction, the relationship humans have with the microorganisms that live within the body – the microbiota – is a critical one for understanding the ramifications of human activity in the past.
Advancing oral microbiome research has revealed the association between oral microbiome composition and oral disease. However, much of the research has predominantly focused on comparing health and disease conditions, overlooking the potential dental public health implications. This article examines the evolution of oral microbial research from inception, advancement, and current knowledge of health-associated microbiota. Specifically, we focus on two key aspects: the impact of lifestyle and environmental factors on the oral microbiome and using the oral microbes as a therapeutic modality. The complex interaction of host intrinsic, environmental, and lifestyle factors affects the occurrence and development of the oral microbiota. The article highlights the need for ongoing research that embraces population diversity to promote health equity in oral health research and integrate public health practices into microbiome-based research. The implication of population-level interventions and targeted approaches harnessing the oral microbiome as an intervention, such as oral microbiome transplantation, should be further explored.
It is known that the bacterial gut microbiome is altered in inflammatory bowel disease (IBD), but far less is known about the role of eukaryotic microorganisms in IBD. While eukaryotes are rarer than bacteria within the gastrointestinal environment, the current literature suggests that they may also be implicated in IBD. In our study, we characterized these often-neglected eukaryotic microbial communities by identifying fungi and protozoa in published shotgun stool metagenomes from 355 people with IBD (206 with Crohn's disease, 126 with ulcerative colitis, and 23 with IBD-unclassified) and 471 unaffected healthy individuals. The individuals with IBD had a higher prevalence of fungi, particularly Saccharomyces cerevisiae, and a lower prevalence of protozoa, particularly Blastocystis species (subtypes 1, 2, 3, and 4). Regression analysis showed that disease state, age, and BMI were associated with the prevalence and abundance of these two genera. We also characterized the eukaryotic gut microbiome in a shotgun stool metagenomic dataset from people with IBD who received fecal transplants, with samples pre- and post-transplantation, and from their donors. We found that in some FMT recipients, a single eukaryotic species remained stable over time, while in other recipients, the eukaryotic composition varied. We conclude that the eukaryotic gut microbiome is altered and varies over time in IBD, and future studies should aim to include these microbes when characterizing the gut microbiome in IBD.
The field of palaeomicrobiology-the study of ancient microorganisms-is rapidly growing due to recent methodological and technological advancements. It is now possible to obtain vast quantities of DNA data from ancient specimens in a high-throughput manner and use this information to investigate the dynamics and evolution of past microbial communities. However, we still know very little about how the characteristics of ancient DNA influence our ability to accurately assign microbial taxonomies (i.e. identify species) within ancient metagenomic samples. Here, we use both simulated and published metagenomic data sets to investigate how ancient DNA characteristics affect alignment-based taxonomic classification. We find that nucleotide-to-nucleotide, rather than nucleotide-to-protein, alignments are preferable when assigning taxonomies to short DNA fragment lengths routinely identified within ancient specimens (<60 bp). We determine that deamination (a form of ancient DNA damage) and random sequence substitutions corresponding to ∼100,000 years of genomic divergence minimally impact alignment-based classification. We also test four different reference databases and find that database choice can significantly bias the results of alignment-based taxonomic classification in ancient metagenomic studies. Finally, we perform a reanalysis of previously published ancient dental calculus data, increasing the number of microbial DNA sequences assigned taxonomically by an average of 64.2-fold and identifying microbial species previously unidentified in the original study. Overall, this study enhances our understanding of how ancient DNA characteristics influence alignment-based taxonomic classification of ancient microorganisms and provides recommendations for future palaeomicrobiological studies.
Santiago-Rodriguez et al. [1] report on the putative gut microbiome and resistome of Inca and Italian mummies, and find that Italian mummies exhibit higher bacterial diversity compared to the Inca mummies.[...].
The high prevalence of dental caries and periodontal disease place a significant burden on society, both socially and economically. Recent advances in genomic technologies have linked both diseases to shifts in the oral microbiota - a community of >700 bacterial species that live within the mouth. The development of oral microbiome transplantation draws on the success of fecal microbiome transplantation for the treatment of gut pathologies associated with disease. Many current in vitro oral biofilm models have been developed but do not fully capture the complexity of the oral microbiome which is required for successful OMT. To address this, we developed an in vitro biofilm system that maintained an oral microbiome with 252 species on average over 14 days. Six human plaque samples were grown in 3D printed flow cells on hydroxyapatite discs using artificial saliva medium (ASM). Biofilm composition and growth were monitored by high throughput sequencing and confocal microscopy/SEM, respectively. While a significant drop in bacterial diversity occurred, up to 291 species were maintained in some flow cells over 14 days with 70% viability grown with ASM. This novel in vitro biofilm model represents a marked improvement on existing oral biofilm systems and provides new opportunities to develop oral microbiome transplant therapies.
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