Ecological and Evolutionary Science

Archaea:
a Neglected Group in the Microbial World?

The original article can be found here.

A recent study by Raymann et al. (2017) reports that universal 16S primers are biased toward amplification of bacteria because they fail to detect a majority of archaeal diversity in intestinal microbial communities. In great apes, primers specifically targeting the V4 and V5 regions of the archaeal 16S rRNA gene revealed a substantial increase in the detection of operation taxonomic units (OTUs) of archaea, the vast majority of which are methanogenic. Interestingly, both bacterial diversity and archaeal diversity appear to have been lost during great ape diversification.

Recent years have witnessed a boom in the description of symbiotic microbial communities in eukaryotic hosts, thanks in large part to the application of universal primers (short strands of DNA that target specific genes) and high-throughput sequencing capabilities. Although these universal primers can supposedly detect both bacteria and archaea, evidence suggests that archaeal diversity has been dramatically underestimated in most microbiome studies. This is due to the bias toward bacteria of the most commonly used primers (e.g., 516F and 806R, which target the V4 region of the 16S rRNA gene). Indeed, when archaeon-specific primers were applied to gut samples from great apes (humans, chimps, bonobos, gorillas, and orangutans), a >10-fold increase in archaeal diversity over that detected by conventional 16S primers was observed. Furthermore, many of the archaeal microbes detected in great ape samples represent novel diversity at the genus and species levels. Although the issue of underestimating archaeal diversity has been recognized previously, few studies have attempted to address the issue directly.

One reason that archaea have taken a back seat to bacteria in microbiome studies is, perhaps, the fact that there are no known archaeal pathogens. Such being the case, archaea are rarely mentioned in clinically oriented microbiology courses, despite the fact that they have been known for at least 2 decades to persist in the human gut. From a clinical perspective, this might seem reasonable. However, by our neglecting to study archaeal-human interactions, it is quite possible that important information has been overlooked and that clinical symptoms have improperly been attributed to bacterial-human interactions or dysbioses. Take, for example, the finding by Oxley et al. (2010) of diverse lineages of Halobacteriaceae (archaea that persist in extremely salty environments) in the intestinal lumens of patients afflicted with inflammatory bowel disease or the association found by Horz et al. (2012) of Thermoplasmatales archaea (archaea that persist in very acidic environments) with subgingival plaque in patients suffering from periodontitis. Alternatively, Brugére et al. (2014) suggest that some archaeal methanogens might be useful as treatments for human metabolic disorders.

Most studies of gut microbiota have focused on humans or species of industrial importance (cows, poultry, etc.). Archaeal diversity identified in these studies is typically limited to methanogens, with occasional detection of Halobacteriales. Evidence from small surveys of other primarily herbivorous vertebrates suggests that methanogens are the predominant archaea in the guts of other animals as well. Whether this is due to primer bias and whether this result holds true for nonherbivorous species remain to be explored for most wild animals. A recent survey by Sanders et al. (2015) of whale microbiota detected a substantial abundance of methanogens belonging to an archaeal order different from that found most frequently in other mammals (Methanomassiliicoccales in baleen whales versus Methanobacteria in other mammals). Despite this difference, the study’s metagenomic analyses revealed a high level of functional similarity between the whale microbiomes and microbiomes of terrestrial herbivorous relatives.

In the case of rare or endangered species, samples for microbial analyses can be difficult to obtain, and thus opportunities to sample microbial diversity are quite rare. Such is the case with whales, for example, or with wild mountain gorillas like those examined in the great ape study. Such studies typically depend on collection of fecal material from the animals’ environment rather than from direct sampling of the hosts themselves. It is therefore important to consider maximizing the information obtained from each individual sample. In addition to ensuring that archaeal diversity as well as bacterial diversity is adequately assessed, it would be prudent to survey fungal and viral diversity in such cases. To this end, many museums have begun preserving biological samples from the field in various ways conducive to different types of analyses (e.g., cryogenic preservation, storage in RNA-preserving buffers, and FTA cards [buffer-treated paper originally designed for forensic applications]). In this way, museum and field biologists can ensure that maximal data are obtained from rare samples or from those that are difficult to obtain (read more about these methods here).

Archaea have not gone completely undetected in previous studies, of course, and the new data from the recent great apes study mirror previous work by revealing that the vast majority of archaea detected in humans and other primates are methanogens. Interestingly, this study also noted substantial diversity among Thaumarchaeota, which consist primarily of ammonia-oxidizing archaea. Such revelations underscore the importance of selecting the appropriate tools to reduce bias when drawing conclusions about the presence or absence of microbial diversity in a given community. Perhaps more excitingly, these findings highlight the fact that a vast amount of archaeal diversity is yet to be discovered in studies of gut (and other) microbial communities.

References:

Brugere JF, Borrel G, Gaci N, Tottey W, O’Toole PW, et al. (2014) Archaebiotics: proposed therapeutic use of archaea to prevent trimethylaminuria and cardiovascular disease. Gut Microbes 5: 5–10. doi: 10.4161/gmic.26749. pmid:24247281

Horz HP, Seyfarth I, Conrads G (2012) McrA and 16S rRNA gene analysis suggests a novel lineage of Archaea phylogenetically affiliated with Thermoplasmatales in human subgingival plaque. Anaerobe 18: 373–377. doi: 10.1016/j.anaerobe.2012.04.006. pmid:22561061

Sanders JG, Beichman AC, Roman J, Scott JJ, Emerson D, McCarthy JJ, Girguis PR (2015) Baleen whales host a unique gut microbiome with similarities to both carnivores and herbivores. Nature Communications 6:8285. doi: 10.1038/ncomms9285.

Oxley AP, Lanfranconi MP, Wurdemann D, Ott S, Schreiber S, et al. (2010) Halophilic archaea in the human intestinal mucosa. Environ Microbiol 12: 2398–2410. doi: 10.1111/j.1462-2920.2010.02212.x. pmid:20438582.

Tags

5 Comments

katherine.larochelle

2017-06-04 11:41:27

There was a super cool lecture on this topic at ASMicrobe yesterday!

Ketema Bacha

2017-05-02 02:58:58

Very Interesting/

    RantheMan21

    2017-06-04 10:38:37

    What an amazing article to look at and get a new idea on microbiology!

    katherine.larochelle

    2017-06-04 11:43:17

    Agreed; often we spend a very significant amount of time on bacteria and not a significant amount of time on archaea. Who are we to say that archaea are less important to study? Hoping to have more discussions about archaea in the near future!

2017-04-12 10:43:12

Great Read!

Comments are closed.