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A New Piece in the Microbiome Puzzle Lindsay J NEWS & ANALYSIS GENOME WATCH A new piece in the microbiome puzzle Lindsay J. Pike and Samuel C. Forster This month’s Genome Watch discusses Raymann et al. reported a progressive reduc- associated with soil, was found in the lung the detailed analysis of the human tion in archaeal diversity between more dis- environment. The Methanobacterium genus, ‘archaeome’ from various body sites tantly related apes and humans2, a finding that also a member of the DPANN superphylum and highlights how current sequencing was also previously described for the bacterial that is typically associated with anaerobic methods underestimate archaeal diversity component of the human microbiome. These digesters, was identified in biopsies of the and abundance. data further suggest that archaeal diversity ileum and left colon. These observations sug- and prevalence in humans may have been gest that archaea may contribute to the human The human microbiome is inextricably underestimated to date. microbiome in currently unknown ways. linked with our health as well as disease states To accurately assess the archaeal com- In summary, studies using tailored and conditions. The bacterial component ponent of the gastrointestinal tract (GIT), approaches to specifically study archaea have of the human microbiota has been the main nose, lung and skin microbiome, Koskinen uncovered the vast diversity and abundance of focal point of study owing to its abundance, et al. analysed the sequences resulting from archaea in the human microbiota and discov- although studies of viruses, fungi and micro- amplification with archaeal-specific primers. ered previously unseen similarities between scopic eukaryotes and archaea are increasing. Conventional analysis with the Mothur and archaea and bacteria, including distinct Archaea specifically are reported to occur in Qiime software packages produced 400–600 bio geographical communities and higher most individuals and may represent in excess archaeal OTUs. In contrast, application of the diversity in more evolutionarily ancient apes of 10% of the anaerobic microorganisms in the more stringent DADA2 software detected compared with humans. Future studies using large intestine. Methanoarchaea are hypoth- only 10–20 OTUs. DADA2 (REF. 3) differs unbiased shotgun metagenomic or specific esized to be ‘keystone species’ in metabolic from traditional OTU clustering by model- archaea-targeting methods are important processes in the gut. In addition, associations ling and correcting Illumina amplicon errors to elucidate the role of archaea in the human between the presence of certain archaea and and then using the corrected sequences to microbiome and additional similarities or conditions such as irritable bowel disease have detect ribosomal sequence variants. Using this differences with the bacterial component of been noted. Despite this importance, only approach, the authors discovered a biogeo- the human microbiome. limited research has focused on the role of graphical landscape, with the skin and GIT Lindsay J. Pike is at the Sanger Institute, Wellcome archaea, possibly due to the absence of known being characterized by distinct archaeal phyla Trust Genome Campus, Hinxton, Cambridge CB10 1SA, archaeal pathogens or the poor recovery of and the nose sharing phyla with both these UK. Samuel C. Forster is at the Sanger Institute, archaeal species in microbiome studies. communities. Notably, a similar distribution Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK; and the Hudson Institute of Medical 1 In their recent paper, Koskinen et al. of bacterial communities was reported by the Research, Clayton, Victoria 3168, Australia. report that specific archaeal communities are Human Microbiome Project4. Furthermore, e‑mail: [email protected] associated with different sites in the human spatial distributions of archaea have been doi:10.1038/nrmicro.2018.24 body. Previously, studies of archaea in humans reported in several other environments, Published online 19 Feb 2018 have typically been limited to what is recov- often linked to microclimate, including ele- 1. Koskinen, K. et al. First insights into the diverse ered from ‘universal’ 16S rRNA profiling, vation on Mount Fuji5 and oil pollution in human archaeome: specific detection of Archaea in 6 the gastrointestinal tract, lung, and nose and on skin. designed to target broad ranges of bacteria Sundarbans mangroves . mBio 8, e00824-00817 (2017). and some archaea. Koskinen et al. demon- The optimized approach used by 2. Raymann, K. et al. Unexplored archael diversity in the great ape gut microbiome. mSphere 2, https://doi.org/ strate that the universal primers are inefficient Koskinen et al. identified the presence of 10.1128/mSphere.00026-17 (2017). in recovering archaea from the human micro- archaeal species that were not previously 3. Callahan, B. J. et al. DADA2: high-resolution sample inference from Illumina amplicon data. Nat. Methods biome. The universal primers only detected thought to be associated with humans. For 13, 581–583 (2016). a single archaeal operational taxonomic unit example, Woesearcheota, a member of the 4. The Human Microbiome Project Consortium. Structure, function and diversity of the healthy human (OTU) in a human stool sample, whereas DPANN (Diapherotrites, Parvarchaeota, microbiome. Nature 486, 207–214 (2012). archaeal 16S rRNA-specific primers detected Aenigmarchaeota, Nanoarchaeota and 5. Singh, D., Takahashi, K. & Adams, J. M. Elevational patterns in archaeal diversity on Mt. Fuji. PLoS ONE higher numbers and more diverse archaeal Nanohaloarchaeota) superphylum typically 7, e44494 (2012). OTUs. A study of the gut archaeome of five 6. Bhattacharyya, A. et al. Diversity and distribution of 2 archaea in the Mangrove sediment of Sundarbans. great ape species reported similar results archaea. Archaea 2015, 968582 (2015). when comparing the same universal primers Competing interests statement against archaeal-specific primers. Moreover, The authors declare no competing interests. Philip Patenall/ Macmillan Publishers Limited 186 | APRIL 2018 | VOLUME 16 www.nature.com/nrmicro ©2018 Mac millan Publishers Li mited, part of Spri nger Nature. All ri ghts reserved. .
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