Page 20 - Read Online

Page 2 of 15 Ladeira et al. Microbiome Res Rep 2023;2:9 https://dx.doi.org/10.20517/mrr.2023.01

Conclusion: This study expands our knowledge of the ecology and variability of the Bifidobacterium community,
particularly in adults, and its specific association with the gut microbiota and health. Its findings may guide the
rational selection of Bifidobacterium strains for gut microbiome complementation according to the individual’s
endogenous Bifidobacterium community. Our results also suggest that gut microbiome stratification for particular
genera may be relevant for studies of variations of species and associations with the gut microbiome and health.

Keywords: Human gut microbiome, Bifidobacterium longum, Bifidobacterium adolescentis, partitions, function, MAGs,
health

INTRODUCTION
Bifidobacterium is a gut microbiome component, the abundance of which varies with age and health status.
Many studies have shown that various metabolic, immune, and intestinal disease states coincide with
Bifidobacterium depletion from the human gut microbiota . Bifidobacterium species metabolize a wide
[1]
[2]
range of simple and complex glycans, some dietary and others host-derived , and produce various
metabolites, such as organic acids, B vitamins , tryptophan-derived metabolites , and neurotransmitters,
[3]
[4]
such as GABA . As such, Bifidobacterium performs a number of roles in interactions between the gut
[5]
microbiota and the host. The prevalence of Bifidobacterium species varies considerably during the lifespan
of an individual human, particularly between infancy and adulthood. The abundance and prevalence of B.
bifidum, B. breve, B. longum subsp. Longum, are typically high in the infant gut microbiota across different
populations with variation for B. longum subsp. infantis . The prevalence of Bifidobacterium generally
[6-8]
[9]
exceeds 90% in healthy adults, with just a few species present per subject , mostly B. adolescentis and B.
longum subsp longum (B. longum), which are able to metabolize complex dietary carbohydrates . The
[10]
Bifidobacterium content of the human gut microbiome has been well studied in both healthy and diseased
individuals and following dietary interventions, but little is known about the variability of Bifidobacterium
species between subjects and its effects on gut microbiome composition, function, and human health. Most
cross-sectional or interventional studies performed to date have had a limited sample size, with potentially
restricted variation in the gut microbiome, including that for Bifidobacterium communities. Over the last
decade, large cross-sectional cohorts (> 1,000 subjects) have been established and studied to disentangle the
specific associations between intrinsic and extrinsic factors and the gut microbiome. For instance, the
abundance of Bifidobacterium has been shown to depend on genetics, specifically lactase persistence/non-
persistence , and dietary factors, such as carbohydrates [11,12] . Despite their significant relevance for
[11]
identifying the major factors underlying gut microbiome variation, some single cohorts may display a lack
of gut microbiome variation as a function of health status, lifestyle, age, and taxonomic and functional
resolution.

The use of public databases containing large amounts of human gut microbiota shotgun metagenomic data
spanning different ages, countries, health statuses, and lifestyles has greatly increased in recent years,
providing new insight into the association of the gut microbiota with the host, environmental factors, and
the reconstruction of metagenome-assembled genomes (MAGs) [13-18] . An extensive study by Pasolli et al.
[16]
yielded over 150.000 MAGs . Large-scale analyses of targeted bacterial species have improved our
understanding of their diversity, ecology, and association with health and lifestyle. For instance, the study of
a
Faecalibacterium prausnitzii , Akkermansia muciniphila , n d Prevotella copri h a s r e v e a l e d n e w
[21]
[20]
[19]
diversity and specific functional features associated with the host and environmental factors. Despite the
increasing availability of metagenomic data, we still know very little about the metabolic contributions of
strains within an ecological niche. Strains of Bifidobacterium have long been considered of major interest
for use as probiotics [22,23] , but the variability and ecology of resident Bifidobacterium species and their
association with the host and the gut microbiome have been little explored in large-scale studies. One recent