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Cited by 303Probiotics and Fermented FoodsGut microbiota and healthReproductive tract infections research

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The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health

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De Filippis, Francesca, Pasolli, Edoardo, Ercolini, Danilo·2020·FEMS Microbiology Reviews
DOI 10.1093/femsre/fuaa015PMC PMC7391071
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Abstract

Lactic acid bacteria (LAB) are present in foods, the environment and the animal gut, although fermented foods (FFs) are recognized as the primary niche of LAB activity. Several LAB strains have been studied for their health-promoting properties and are employed as probiotics. FFs are recognized for their potential beneficial effects, which we review in this article. They are also an important source of LAB, which are ingested daily upon FF consumption. In this review, we describe the diversity of LAB and their occurrence in food as well as the gut microbiome. We discuss the opportunities to study LAB diversity and functional properties by considering the availability of both genomic and metagenomic data in public repositories, as well as the different latest computational tools for data analysis. In addition, we discuss the role of LAB as potential probiotics by reporting the prevalence of key genomic features in public genomes and by surveying the outcomes of LAB use in clinical trials involving human subjects. Finally, we highlight the need for further studies aimed at improving our knowledge of the link between LAB-fermented foods and the human gut from the perspective of health promotion.

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Crossref · 10.1093/femsre/fuaa015

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Figure 1. Bubble plot showing prevalence (% of samples) of LAB genera and species in different fermented foods, as obtained from 16S rRNA gene sequencing studies reported in FoodMicrobionet (Parente et al. 2019). A taxon was considered present if its relative abundance was > 0.5%. For lactobacilli, species were grouped into taxonomic groups, as reported by Salvetti et al. (2018).
Figure 1. Bubble plot showing prevalence (% of samples) of LAB genera and species in different fermented foods, as obtained from 16S rRNA gene sequencing studies reported in FoodMicrobionet (Parente et al. 2019). A taxon was considered present if its relative abundance was > 0.5%. For lactobacilli, species were grouped into taxonomic groups, as reported by Salvetti et al. (2018).CC BY · PubMed Central
Figure 2. Number of LAB reference genomes in NCBI grouped at (A) genera and (B) species level. In (B), only species with at least 10 genomes deposited in NCBI on December 2019 are shown.
Figure 2. Number of LAB reference genomes in NCBI grouped at (A) genera and (B) species level. In (B), only species with at least 10 genomes deposited in NCBI on December 2019 are shown.CC BY · PubMed Central
Figure 3. Pie charts showing isolation source for public genomes (available on NCBI in December 2019) of 18 selected LAB species, chosen for their importance in fermented foods and/or as probiotic. NA, Not Available. According to the taxonomy update proposed by Zheng et al. (2020), the names of the genera reported would change as follows: Lb. brevis = Levilactobacillus brevis; Lb casei, Lb. paracasei and Lb. rhamnosus = Lacticaseibacillus spp.; Lb. fermentum and Lb. reuteri = Limosilactobacillus spp.; Lb. sakei and Lb. curvatus = Latilactobacillus spp.; Lb. plantarum and Lb. pentosus = Lactiplantibacillus spp.; Lb. salivarius = Ligilactobacillus.
Figure 3. Pie charts showing isolation source for public genomes (available on NCBI in December 2019) of 18 selected LAB species, chosen for their importance in fermented foods and/or as probiotic. NA, Not Available. According to the taxonomy update proposed by Zheng et al. (2020), the names of the genera reported would change as follows: Lb. brevis = Levilactobacillus brevis; Lb casei, Lb. paracasei and Lb. rhamnosus = Lacticaseibacillus spp.; Lb. fermentum and Lb. reuteri = Limosilactobacillus spp.; Lb. sakei and Lb. curvatus = Latilactobacillus spp.; Lb. plantarum and Lb. pentosus = Lactiplantibacillus spp.; Lb. salivarius = Ligilactobacillus.CC BY · PubMed Central
Figure 4. Heat plot showing prevalence of genes involved in resistance to the GIT passage and engraftment in the gut in public genomes (available on NCBI in December 2019) of 18 selected LAB species, chosen for their importance in fermented foods and/or as probiotic. Eps, genes involved in exopolysaccharides production; ure, urease; bsh, bile-salt hydrolase; luxS, S-ribosylhomocysteine lyase. A list of the genes included and their NCBI accession numbers are reported in Supplementary Table S4. Color bar indicates assignment to the different taxonomic groups, as reported by Salvetti et al. (2018). For the taxonomy update proposed by Zheng et al. (2020), see Figure 3 legend.
Figure 4. Heat plot showing prevalence of genes involved in resistance to the GIT passage and engraftment in the gut in public genomes (available on NCBI in December 2019) of 18 selected LAB species, chosen for their importance in fermented foods and/or as probiotic. Eps, genes involved in exopolysaccharides production; ure, urease; bsh, bile-salt hydrolase; luxS, S-ribosylhomocysteine lyase. A list of the genes included and their NCBI accession numbers are reported in Supplementary Table S4. Color bar indicates assignment to the different taxonomic groups, as reported by Salvetti et al. (2018). For the taxonomy update proposed by Zheng et al. (2020), see Figure 3 legend.CC BY · PubMed Central

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Research works printed but not linked: 3

  1. Lerche, 1961, Isolierung und differenzierung anaerober Lactobacillaceae aus dem Darm erwachsener Menschen (Beitrag zum Lactobacillus bifidus-Problem), Zentralblatt fur Bakeriologie, Parasitenkunde, Infektionskrankheiten und Hygiene, 180, 324
  2. Parks, 2019, Selection of representative genomes for 24,706 bacterial and archaeal species clusters provide a complete genome-based taxonomy, BioRxiv
  3. Reuter, 1965, Untersuchungen uber die Zusammensetzung und die Beeinflussbarkeit der menschlichen Magen-und Darmflora unter besonderer Berucksichtigung der Laktobazillen, Ernahrungsforsch Ber Mitt, 10, 429

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Metadata

Authors
De Filippis, F., Pasolli, E., & Ercolini, D.
Affiliations
  • Department of Agricultural Sciences, University of Naples Federico II, via Università, 100, 80055, Portici (NA) Italy
  • University of Naples Federico II (IT)
Corresponding author
Ercolini, Danilo
ORCID
Venue
FEMS Microbiology Reviews
Publisher
Oxford University Press (OUP)
Published
2020-06-18
Volume
44
Issue
4
Pages
454-489
ISSN
  • 0168-6445 (ISSN-L)
  • 1574-6976
DOI
10.1093/femsre/fuaa015
PMC
PMC7391071
OpenAlex
W3036864319
Cited by
303
References
361
Citations by year
2026: 42 · 2025: 62 · 2024: 63 · 2023: 54 · 2022: 50 · 2021: 25 · 2020: 6
FWCI
2.85
Type
journal article
Language
en
Open access
Licence
Locations
  • FEMS Microbiology Reviews (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
  • Horizon 2020 (818368)
  • Ministry of Agricultural, Food, Forestry and Tourism Policies (790)
Topics
  • Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
  • Life Sciences › Immunology and Microbiology › Microbiology › Reproductive tract infections research
Keywords
lactic acid bacteria, fermented foods, gut microbiota, probiotics, health promotion, metagenomics, genomic features, clinical trials, human health
MeSH terms
Gastrointestinal Microbiome, Food Microbiology, Health, Humans, Lactobacillales

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