Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
, 5 (2), e00889

Revealing the Bacterial Butyrate Synthesis Pathways by Analyzing (Meta)genomic Data

Revealing the Bacterial Butyrate Synthesis Pathways by Analyzing (Meta)genomic Data

Marius Vital et al. mBio.

Abstract

Butyrate-producing bacteria have recently gained attention, since they are important for a healthy colon and when altered contribute to emerging diseases, such as ulcerative colitis and type II diabetes. This guild is polyphyletic and cannot be accurately detected by 16S rRNA gene sequencing. Consequently, approaches targeting the terminal genes of the main butyrate-producing pathway have been developed. However, since additional pathways exist and alternative, newly recognized enzymes catalyzing the terminal reaction have been described, previous investigations are often incomplete. We undertook a broad analysis of butyrate-producing pathways and individual genes by screening 3,184 sequenced bacterial genomes from the Integrated Microbial Genome database. Genomes of 225 bacteria with a potential to produce butyrate were identified, including many previously unknown candidates. The majority of candidates belong to distinct families within the Firmicutes, but members of nine other phyla, especially from Actinobacteria, Bacteroidetes, Fusobacteria, Proteobacteria, Spirochaetes, and Thermotogae, were also identified as potential butyrate producers. The established gene catalogue (3,055 entries) was used to screen for butyrate synthesis pathways in 15 metagenomes derived from stool samples of healthy individuals provided by the HMP (Human Microbiome Project) consortium. A high percentage of total genomes exhibited a butyrate-producing pathway (mean, 19.1%; range, 3.2% to 39.4%), where the acetyl-coenzyme A (CoA) pathway was the most prevalent (mean, 79.7% of all pathways), followed by the lysine pathway (mean, 11.2%). Diversity analysis for the acetyl-CoA pathway showed that the same few firmicute groups associated with several Lachnospiraceae and Ruminococcaceae were dominating in most individuals, whereas the other pathways were associated primarily with Bacteroidetes. IMPORTANCE Microbiome research has revealed new, important roles of our gut microbiota for maintaining health, but an understanding of effects of specific microbial functions on the host is in its infancy, partly because in-depth functional microbial analyses are rare and publicly available databases are often incomplete/misannotated. In this study, we focused on production of butyrate, the main energy source for colonocytes, which plays a critical role in health and disease. We have provided a complete database of genes from major known butyrate-producing pathways, using in-depth genomic analysis of publicly available genomes, filling an important gap to accurately assess the butyrate-producing potential of complex microbial communities from "-omics"-derived data. Furthermore, a reference data set containing the abundance and diversity of butyrate synthesis pathways from the healthy gut microbiota was established through a metagenomics-based assessment. This study will help in understanding the role of butyrate producers in health and disease and may assist the development of treatments for functional dysbiosis.

Figures

FIG 1
FIG 1
Four different pathways for butyrate synthesis and corresponding genes (protein names) are displayed. Major substrates are shown. Terminal genes are highlighted in red. L2Hgdh, 2-hydroxyglutarate dehydrogenase; Gct, glutaconate CoA transferase (α, β subunits); HgCoAd, 2-hydroxy-glutaryl-CoA dehydrogenase (α, β, γ subunits); Gcd, glutaconyl-CoA decarboxylase (α, β subunits); Thl, thiolase; hbd, β-hydroxybutyryl-CoA dehydrogenase; Cro, crotonase; Bcd, butyryl-CoA dehydrogenase (including electron transfer protein α, β subunits); KamA, lysine-2,3-aminomutase; KamD,E, β-lysine-5,6-aminomutase (α, β subunits); Kdd, 3,5-diaminohexanoate dehydrogenase; Kce, 3-keto-5-aminohexanoate cleavage enzyme; Kal, 3-aminobutyryl-CoA ammonia lyase; AbfH, 4-hydroxybutyrate dehydrogenase; AbfD, 4-hydroxybutyryl-CoA dehydratase; Isom, vinylacetyl-CoA 3,2-isomerase (same protein as AbfD): 4Hbt, butyryl-CoA:4-hydroxybutyrate CoA transferase; But, butyryl-CoA:acetate CoA transferase; Ato, butyryl-CoA:acetoacetate CoA transferase (α, β subunits); Ptb, phosphate butyryltransferase; Buk, butyrate kinase. Cosubstrates for individual butyryl-CoA transferases are shown.
FIG 2
FIG 2
A list of all obtained candidate bacteria and their taxonomic classifications. Firmicutes are shown in panel A, whereas candidates associated with other phyla are displayed in panel B. Names in bold represent known butyrate-producing strains. Origins of isolates (Isol.), where brown refers to human/animal-associated strains (individual body sites of isolation are as follows: GI, gastrointestinal tract; UG, urogenital tract; O, oral tract) and green to environmental isolates, are given. Individual pathways with corresponding final genes are shown, namely, the acetyl-CoA pathway (AceCoA; orange-yellow) and the glutarate pathway (Gltr; blue) with but (encoding butyryl-CoA:acetate CoA transferase; red; light pink represents “atypical” transferases) and buk (butyrate kinase; red), as well as the 4-aminobutyrate pathway (4-Amin; pink) with the 4Hbt gene (butyryl-CoA:4-hydroxybutyrate CoA transferase; red) and the lysine pathway (Lys; grey) with ato (encoding butyryl-CoA:acetoacetate CoA transferase). Results of synteny analysis for genes of individual pathways are indicated (see key to color patterns at the bottom). Black cells in the column “Bcd-αβ” represent the presence of the butyryl-CoA dehydrogenase electron transfer protein complex, i.e., bcd is in synteny with the etf genes. Names in red indicate isolates that are reported to oxidize butyrate for growth. Actinob., Actinobacteria; Spro., Spirochaetes; The., Thermotogae; Bact., Bacteroidetes; C. Incertae Sedis, Clostridiales incertae sedis. For more explanation, see the text.
FIG 2
FIG 2
A list of all obtained candidate bacteria and their taxonomic classifications. Firmicutes are shown in panel A, whereas candidates associated with other phyla are displayed in panel B. Names in bold represent known butyrate-producing strains. Origins of isolates (Isol.), where brown refers to human/animal-associated strains (individual body sites of isolation are as follows: GI, gastrointestinal tract; UG, urogenital tract; O, oral tract) and green to environmental isolates, are given. Individual pathways with corresponding final genes are shown, namely, the acetyl-CoA pathway (AceCoA; orange-yellow) and the glutarate pathway (Gltr; blue) with but (encoding butyryl-CoA:acetate CoA transferase; red; light pink represents “atypical” transferases) and buk (butyrate kinase; red), as well as the 4-aminobutyrate pathway (4-Amin; pink) with the 4Hbt gene (butyryl-CoA:4-hydroxybutyrate CoA transferase; red) and the lysine pathway (Lys; grey) with ato (encoding butyryl-CoA:acetoacetate CoA transferase). Results of synteny analysis for genes of individual pathways are indicated (see key to color patterns at the bottom). Black cells in the column “Bcd-αβ” represent the presence of the butyryl-CoA dehydrogenase electron transfer protein complex, i.e., bcd is in synteny with the etf genes. Names in red indicate isolates that are reported to oxidize butyrate for growth. Actinob., Actinobacteria; Spro., Spirochaetes; The., Thermotogae; Bact., Bacteroidetes; C. Incertae Sedis, Clostridiales incertae sedis. For more explanation, see the text.
FIG 3
FIG 3
Simplified representations of neighbor-joining trees of individual genes (protein sequences) are shown. The left column in each tree shows arrangement of different genes associated with different families within the phylum Firmicutes, whereas gene entries linked to other phyla are given in the right column. For a key to colors see the bottom. Letters (A to D) represent the four distinct regions of individual trees based on genes of the acetyl-CoA pathway, and “*” marks deviations from the overall trend. For an explanation, see the text.
FIG 4
FIG 4
Abundance of butyrate-producing pathways (calculated as a percentage of total bacterial genomes theoretically exhibiting a pathway) in metagenomic data from stool samples of 15 healthy humans is shown. Different colors represent individual pathways (acetyl-CoA pathway, orange; glutarate pathway, blue; 4-aminobutyrate pathway, pink; lysine pathway, grey). The box plot displays the data distribution for all 15 samples analyzed (A to O).
FIG 5
FIG 5
The detected diversity in metagenomic data associated with individual pathways. Colors correspond to different pathways (acetyl-CoA pathway, orange; glutarate pathway, blue; 4-aminobutyrate pathway, pink; lysine pathway, grey). Bacterial names represent members of individual groups (based on 10% complete linkage clustering; for details, see Materials and Methods). Groups consist of the following: (i) only one reference genome (indicated by single strain names), (ii) merged strains of the same species (indicated by species name without strain information), and (iii) merged genomes from distinct species (individual names are given). The group “Fusobacteria several strains” consists of the following strains: Fusobacterium nucleatum subsp. nucleatum, Fusobacterium nucleatum subsp. polymorphum ATCC 10953, Fusobacterium periodonticum ATCC 33693, sp. 1_1_41FAA, sp. 11_3_2, sp. 2_1_31, sp. 21_1A, sp. 3_1_27, sp. 3_1_33, sp. 3_1_36A2, sp. 4_1_13, sp. 7_1, sp. D11, and sp. D12. For more information on taxon assignment, see Materials and Methods. The box plots display data distributions for each group of all 15 samples analyzed (A to O). The degree of explanation indicates the percentages of reads matching a group, which was included in diversity analysis (this figure). For more explanation, see the text.

Similar articles

See all similar articles

Cited by 123 PubMed Central articles

See all "Cited by" articles

References

    1. Sørensen J, Christensen D, Jørgensen BB. 1981. Volatile fatty acids and hydrogen as substrates for sulfate-reducing bacteria in anaerobic marine sediment. Appl. Environ. Microbiol. 42:5–11 - PMC - PubMed
    1. Paillard D, McKain N, Chaudhary LC, Walker ND, Pizette F, Koppova I, McEwan NR, Kopecný J, Vercoe PE, Louis P, Wallace RJ. 2007. Relation between phylogenetic position, lipid metabolism and butyrate production by different Butyrivibrio-like bacteria from the rumen. Antonie Van Leeuwenhoek 91:417–422. 10.1007/s10482-006-9121-7 - DOI - PubMed
    1. Shah HN, Williams RA, Bowden GH, Hardie JM. 1976. Comparison of the biochemical properties of Bacteroides melaninogenicus from human dental plaque and other sites. J. Appl. Bacteriol. 41:473–495. 10.1111/j.1365-2672.1976.tb00660.x - DOI - PubMed
    1. Pryde SE, Duncan SH, Hold GL, Stewart CS, Flint HJ. 2002. The microbiology of butyrate formation in the human colon. FEMS Microbiol. Lett. 217:133–139. 10.1111/j.1574-6968.2002.tb11467.x - DOI - PubMed
    1. Hamer HM, Jonkers D, Venema K, Vanhoutvin S, Troost FJ, Brummer RJ. 2008. Review article: the role of butyrate on colonic function. Aliment. Pharmacol. Ther. 27:104–119. 10.1111/j.1365-2036.2007.03562.x - DOI - PubMed

Publication types

Feedback