Dataset Information

Exploring the Archaeome: Detection of Archaeal Signatures in the Human Body.

ABSTRACT: Due to their fundamentally different biology, archaea are consistently overlooked in conventional microbiome surveys. Using amplicon sequencing, we evaluated methodological set-ups to detect archaea in samples from five different body sites: respiratory tract (nasal cavity), digestive tract (mouth, appendix, and stool) and skin. With optimized protocols, the detection of archaeal ribosomal sequence variants (RSVs) was increased from one (found in currently used, so-called "universal" approach) to 81 RSVs in a representative sample set. The results from this extensive primer-evaluation led to the identification of the primer pair combination 344f-1041R/519F-806R which performed superior for the analysis of the archaeome of gastrointestinal tract, oral cavity and skin. The proposed protocol might not only prove useful for analyzing the human archaeome in more detail but could also be used for other holobiont samples.

SUBMITTER: Pausan MR

PROVIDER: S-EPMC6906140 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Exploring the Archaeome: Detection of Archaeal Signatures in the Human Body.

Pausan Manuela R MR Csorba Cintia C Singer Georg G Till Holger H Schöpf Veronika V Santigli Elisabeth E Klug Barbara B Högenauer Christoph C Blohs Marcus M Moissl-Eichinger Christine C

Frontiers in microbiology 20191205

Due to their fundamentally different biology, archaea are consistently overlooked in conventional microbiome surveys. Using amplicon sequencing, we evaluated methodological set-ups to detect archaea in samples from five different body sites: respiratory tract (nasal cavity), digestive tract (mouth, appendix, and stool) and skin. With optimized protocols, the detection of archaeal ribosomal sequence variants (RSVs) was increased from one (found in currently used, so-called "universal" approach) t ...[more]

PMID: 31866971

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Project description:Human-associated archaea remain understudied in the field of microbiome research, although in particular methanogenic archaea were found to be regular commensals of the human gut, where they represent keystone species in metabolic processes. Knowledge on the abundance and diversity of human-associated archaea is extremely limited, and little is known about their function(s), their overall role in human health, or their association with parts of the human body other than the gastrointestinal tract and oral cavity. Currently, methodological issues impede the full assessment of the human archaeome, as bacteria-targeting protocols are unsuitable for characterization of the full spectrum of Archaea The goal of this study was to establish conservative protocols based on specifically archaea-targeting, PCR-based methods to retrieve first insights into the archaeomes of the human gastrointestinal tract, lung, nose, and skin. Detection of Archaea was highly dependent on primer selection and the sequence processing pipeline used. Our results enabled us to retrieve a novel picture of the human archaeome, as we found for the first time Methanobacterium and Woesearchaeota (DPANN superphylum) to be associated with the human gastrointestinal tract and the human lung, respectively. Similar to bacteria, human-associated archaeal communities were found to group biogeographically, forming (i) the thaumarchaeal skin landscape, (ii) the (methano)euryarchaeal gastrointestinal tract, (iii) a mixed skin-gastrointestinal tract landscape for the nose, and (iv) a woesearchaeal lung landscape. On the basis of the protocols we used, we were able to detect unexpectedly high diversity of archaea associated with different body parts.IMPORTANCE In summary, our study highlights the importance of the primers and data processing pipeline used to study the human archaeome. We were able to establish protocols that revealed the presence of previously undetected Archaea in all of the tissue samples investigated and to detect biogeographic patterns of the human archaeome in the gastrointestinal tract and on the skin and for the first time in the respiratory tract, i.e., the nose and lungs. Our results are a solid basis for further investigation of the human archaeome and, in the long term, discovery of the potential role of archaea in human health and disease.

Project description:Human microbiome studies remain focused on bacteria, as they comprise the dominant component of the microbiota. Recent advances in sequencing technology and optimization of amplicon sequencing protocols have allowed the description of other members of the microbiome, including eukaryotes (fungi) and, most recently, archaea. There are no known human-associated archaeal pathogens. Their diversity and contribution to health and chronic respiratory diseases, such as chronic rhinosinusitis (CRS), are unknown. Patients with CRS suffer from long-term sinus infections, and while the microbiota is hypothesized to play a role in its pathogenesis, the exact mechanism is poorly understood. In this cross-sectional study, we applied a recently optimized protocol to describe the prevalence, diversity and abundance of archaea in swab samples from the middle meatus of 60 individuals with and without CRS. A nested PCR approach was used to amplify the archaeal 16S rRNA gene for sequencing, and bacterial and archaeal load (also based on 16S rRNA genes) were estimated using Droplet Digital™ PCR (ddPCR). A total of 16 archaeal amplicon sequence variants (ASVs) from the phyla Euryarchaeota and Thaumarchaeota were identified. Archaeal ASVs were detected in 7/60 individuals, independent of disease state, whereas bacterial ASVs were detected in 60/60. Bacteria were also significantly more abundant than archaea. The ddPCR method was more sensitive than amplicon sequencing at detecting archaeal DNA in samples. Phylogenetic trees were constructed to visualize the evolutionary relationships between archaeal ASVs, isolates and clones. ASVs were placed into phylogenetic clades containing an apparent paucity of human-associated reference sequences, revealing how little studied the human archaeome is. This is the largest study to date to examine the human respiratory-associated archaeome, and provides the first insights into the prevalence, diversity and abundance of archaea in the human sinuses.

Project description:Microplastics (MPs) can enter the body via plastic products. Given modern plastic exposure, we seek to assess MP exposure in large populations through epidemiological tools. In this quasi-experimental study, every participant filled out a questionnaire, and those who satisfied any of the following requirements were not allowed to continue in the study: Diabetes, ulcerative colitis, Crohn's disease, infectious diseases. Participants in the exposure and control groups were provided three hot meals in disposable plastic tableware (DPT) (n = 30) or non-DPT (n = 30), respectively. After a month of observation, individuals in the exposure group discontinued the three meals provided in DPT (n = 27) for 1 month as the post-exposure group. Each Participant in the three groups received a questionnaire survey and fecal sample collection. We compared the differences in MP levels between different groups and used the Bland-Altman analysis method to evaluate the consistency of the results obtained by different measurement methods. Statistically significant differences in the total quantity (P (0.80 matching degree) = 0.020; P (0.65 matching degree) < 0.001) and types (Polyethylene Terephthalate (EVA) (P = 0.039), Polyethylene Terephthalate (PET) (P = 0.022), Polyvinyl Butyral (PVB) (P = 0.013), Chlorinated Polyethylene (CPE) (P = 0.039), phenolic epoxy resin (P = 0.012)) of MPs were observed between the exposure and post-exposure groups. The Bland-Altman analysis results indicate that the two methods exhibit good consistency in the three groups (control group: mean difference = 0.54, agreement limits (95% CI) = - 0.44 ~ 1.54; exposure group: mean difference = 0.41, agreement limits (95% CI) = - 0.19 ~ 1.01; post-exposure group: mean difference = 0.19, agreement limits (95% CI) = - 0.63 ~ 1.02). The method based on questionnaire surveys can substitute the method of fecal sample detection to evaluate the exposure of MP particles.

Dataset Information

Exploring the Archaeome: Detection of Archaeal Signatures in the Human Body.

Publications

Exploring the Archaeome: Detection of Archaeal Signatures in the Human Body.

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