Archaeal key-residents within the human microbiome: characteristics, interactions and involvement in health and disease

Mohammadzadeh, Rokhsareh; Mahnert, Alexander; Duller, Stefanie; Moissl-Eichinger, Christine

doi:10.1016/j.mib.2022.102146

Cited by 29 publications

(31 citation statements)

References 81 publications

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“…Due to the unavailability of extensive information on annotations, we focus on understanding the extent to which some of the identified genes were conserved. We specifically assess this in the most abundant human gut archaea, M. smithii , due to its reported role in health and disease [14], [61], [62]. Interestingly, the available MAGs showing HGT events were sampled in different locations (Austria, France, UK, US).…”

Section: Discussionmentioning

confidence: 99%

Functional prediction of proteins from the human gut archaeome

Novikova

Busi

Probst

et al. 2023

Preprint

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The human gastrointestinal tract is a habitat for diverse microbial taxa including archaea. Here, by establishing a unique in silico workflow, we resolve the identities of gut-specific archaeal proteins. We developed a strategy for protein functional annotation employing the most recent protein sequence- and structure-based approaches such as AlphaFold2, trRosetta, ProFunc and DeepFri. Where sequence-based approaches failed, our strategy led to the identification of archaeal proteins. Here, we identify a subset of archaeal gut-specific proteins involved in various defense strategies and virulence. For instance, BglII restriction endonuclease is the most commonly occurring unique protein involved in host genome defense against invading DNA. Furthermore, multiple adhesin-like proteins which likely facilitate archaeal cell adhesion to surfaces. We also resolve functions assisting degradation of toxic substances via propanediol utilization protein pduA. We identify a variety of glycosyltransferases involved in both N-linked glycosylation and O-glycosylation. In addition, we highlight several types of glycosyltransferases encoded by Methanobrevibacter smithii which may possibly be involved in the construction of O-glycosylated surfaces, beneficial for proliferation within the human intestine. Finally, we demonstrate the presence of proteins not only modulating interdomain horizontal gene transfer but also those possibly being the result of such genetic material exchange. In this context, we present evidence on horizontally transferred sporulation stage V proteins AE and AD from Clostridium species to M. smithii. In summary, our tailored in silico workflow allows the characterization of previously undescribed archaeal proteins which are specific to the gut environment and, thus, human microbiome function.

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Section: Discussionmentioning

confidence: 99%

Functional prediction of proteins from the human gut archaeome

Novikova

Busi

Probst

et al. 2023

Preprint

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“…Archaea are commonly found in the human body, especially the gut, accounting for up to 10% of the total anaerobes. − Most of these consist of methanogenic archaea, e.g., M. smithii and M. stadtmanae , with lipids 1 and 2 as membrane components. These lipids are unlikely to be distributed in a monomeric/soluble form.…”

Section: Discussionmentioning

confidence: 99%

“…These prokaryotes were originally found in extreme environments but are now known to be ubiquitous in nature. Archaea are distributed in the human microbiota of the oral cavity, skin, and intestine. − Most human-associated archaea are found in the intestine, which are represented by methanogenic archaea such as Methanobrevibacter smithii and Methanosphaera stadtmanae . − Although archaea were reported approximately 40 years ago to live in the human body, , their relation to host health and diseases remains poorly understood. Particularly, little is known about the molecular entities involved in chemical communication with the host or other symbiotic organisms.…”

Section: Introductionmentioning

confidence: 99%

Archaeal Glycerolipids Are Recognized by C-Type Lectin Receptor Mincle

et al. 2023

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Recently, various metabolites derived from host microbes have been reported to modulate the immune system, with potential involvement in health or diseases. Archaea, prokaryotic organisms, are present in the human body, but their connection with the host is largely unknown when compared to other microorganisms such as bacteria. This study focused on unique glycerolipids from symbiotic methanogenic archaea and evaluated their activities toward an innate immune receptor. The results revealed that archaeal lipids were recognized by the C-type lectin receptor Mincle and induced immune responses. A concurrent structure−activity relationship study identified the key structural features of archaeal lipids required for recognition by Mincle. Subsequent gene expression profiling suggested qualitative differences between the symbiotic archaeal lipid and the pathogenic bacteria-derived lipid. These findings have broad implications for understanding the function of symbiotic archaea in host health and diseases.

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“…Although studies on methanogen metabolites in the context of human health and disease are still relatively new, the occurrence, dynamics, and coincidence of methanogens have been verified to be associated with various diseases, like colorectal cancer and inflammatory bowel disease. 56 Further, it is intriguing that a recent metagenomic study demonstrated that M. smithii was associated with staphylococci from blood and infected human tissues of fever patients and M. smithii was isolated from two of these samples. 57 Although it is possible that M. smithii may coinfect tissues along with staphylococci, this study reinforces the possibility that archaea may contain some disease-related species.…”

Section: Healthmentioning

confidence: 99%

Section: Metabolites Of Methanogens and Human Healthmentioning

confidence: 99%