Low-Abundant Microorganisms: The Human Microbiome’s Dark Matter, a Scoping Review

Abstract

Research on the human microbiome has mainly been restricted to the identification of most abundant microbiota associated with health or disease. Their abundance may reflect their capacity to exploit their niche, however, metabolic functions exerted by low-abundant microrganisms can impact the dysbiotic signature of local microbial habitats. This scoping review aims to map the literature regarding the management of low-abundant microorganisms in studies investigating human microbiome samples. A systematic literature search was performed in 5 electronic databases, as well as grey literature. We selected clinical microbiome studies targeting human participants of any age, from any body site. We also included studies with secondary data which originated from human biofilm samples. All of the papers used next-generation sequencing (NGS) techniques in their methodology. A total of 826 manuscripts were retrieved, of which 42 were included in this review and 22 reported low-abundant bacteria (LB) in samples taken from 7 body sites (breast, gut, oral cavity, skin, stomach, upper respiratory tract (URT), and vagina). Four studies reported microbes at abundance levels between 5 and 20%, 8 studies reported between 1 and 5%, and 18 studies reported below 1%. Fifteen papers mentioned fungi and/or archaea, and from those only 4 (fungi) and 2 (archaea) produced data regarding the abundance of these domains. While most studies were directed towards describing the taxonomy, diversity and abundance of the highly abundant species, low-abundant species have largely been overlooked. Indeed, most studies select a cut-off value at <1% for low-abundant organisms to be excluded in their analyses. This practice may compromise the true diversity and influence of all members of the human microbiota. Despite their low abundance and signature in biofilms, they may generate important markers contributing to dysbiosis, in a sort of ‘butterfly effect’. A detailed snapshot of the physiological, biological mechanisms at play, including virulence determinants in the context of a dysbiotic community, may help better understand the health-disease transition.

Inhibition of Cronobacter sakazakii in an infant simulator of the human intestinal microbial ecosystem using a potential synbiotic

“…Bifidobacterium and other commensal gut microbiota can compete for nutrients with foodborne pathogens (Kamada et al, 2013;O'Callaghan and van Sinderen, 2016), which would further limit the ability for C. sakazakii to grow within the SHIME compartment. Despite the relatively low abundance of some gut microbiota, including Bifidobacterium, our results provide further evidence that the gut microbiota may play a significant biological role through synergistic interactions with other microorganisms (Claussen et al, 2017;Benjamino et al, 2018;Cena et al, 2021).…”

Regulatory effects of oral microbe on intestinal microbiota and the illness

“…Whereas most 16S rRNA gene sequencing analyses only reliably classify taxa to the genus level and do not report species and strains usually. Using shotgun metagenomic sequencing, oral and gut bacterial communities show greater similarity than earlier studies suggested (de Cena et al, 2021;Maki et al, 2021). Moreover, diurnal variations, processing methods, race, and diet are irrelevant interference with measurement results, which requires further consideration in future studies (Superdock and Poole, 2022).…”

Enrichment of sulphate-reducers and depletion of butyrate-producers may be hyperglycaemia signatures in the diabetic oral microbiome

“…Current research on the salivary microbiome has mainly been restricted to the identification of the most abundant microbiota associated with health or disease. We believe that this strategy could cause an incomplete misunderstanding of the ecology and environment as metabolic functions exerted by low-abundant microorganisms can be linked to the dysbiotic microhabitats in a sort of ‘butterfly effect’ [ 58 ]. This can be clearly observed by the inclusion of Desulfobulbus in the analysis, even at very low relative abundance.…”