Metabolite profiling of human-originated Lachnospiraceae at the strain level

Abstract

The human gastrointestinal (GI) tract harbors diverse microbes, and the family Lachnospiraceae is one of the most abundant and widely occurring bacterial groups in the human GI tract. Beneficial and adverse effects of the Lachnospiraceae on host health were reported, but the diversities at species/strain levels as well as their metabolites of Lachnospiraceae have been, so far, not well documented. In the present study, we report on the collection of 77 human-originated Lachnospiraceae species (please refer hLchsp, https://hgmb.nmdc.cn/subject/lachnospiraceae) and the in vitro metabolite profiles of 110 Lachnospiraceae strains (https://hgmb.nmdc.cn/subject/lachnospiraceae/metabolites). The Lachnospiraceae strains in hLchsp produced 242 metabolites of 17 categories. The larger categories were alcohols (89), ketones (35), pyrazines (29), short (C2-C5), and long (C > 5) chain acids (31), phenols (14), aldehydes (14), and other 30 compounds. Among them, 22 metabolites were aromatic compounds. The well-known beneficial gut microbial metabolite, butyric acid, was generally produced by many Lachnospiraceae strains, and Agathobacter rectalis strain Lach-101 and Coprococcus comes strain NSJ-173 were the top 2 butyric acid producers, as 331.5 and 310.9 mg/L of butyric acids were produced in vitro, respectively. Further analysis of the publicly available cohort-based volatile-metabolomic data sets of human feces revealed that over 30% of the prevailing volatile metabolites were covered by Lachnospiraceae metabolites identified in this study. This study provides Lachnospiraceae strain resources together with their metabolic profiles for future studies on host-microbe interactions and developments of novel probiotics or biotherapies.

Keywords: Blautia; Lachnospiraceae; alcohols; aldehydes; metabolite profiling; phenols; short‐chain fatty acids.

Figure 1

Cultivation and collection of Lachnospiraceae isolates for the hLchsp biobank. (A) Distribution at the family level of 1116 bacterial isolates. (B) Uniqueness at the species level of Lachnospiraceae growth on seven culture media. Panels (C) and (D) describe the features of the established hLchsp biobank. (C) Genus names and number of strains of each genus. (D) Species composition of hLchsp biobank. Numbers in the donut chart represent numbers of the species, and species names are provided outside the donut chart when a genus comprises more than one species. Red names represent novel taxa that are newly described in this study. hLchsp, human‐originated Lachnospiraceae species; Lach‐GAM, Lachnospiraceae Gifu Anaerobic medium.

Figure 2

Profiling of metabolites from 110 strains of Lachnospiraceae. (A). Catalogories of 242 metabolites. (B) Shared and unique metabolites among genera of Lachnospiraceae. The inner circle denotes the shared 19 metabolites, and each leaf represents a genus group. The numbers shown on leaves represent genus‐specific metabolites. (C) Heatmap of metabolites from 110 Lachnospiraceae strains. Color describes the relative amounts of metabolites represented with the Log values of peak area; blue to red indicates relative amounts from low to high, strain names in red denoting novel taxa.

Figure 3

Production of SCFAs by Lachnospiraceae strains. Bars in violet, ochre, green, light green, orange, and red represent acetic, propionic, butyric, isobutyric, valeric, and isovaleric acids, respectively; in this scattered bar chart, the height of each bar in different color represents the amount (mg/L) of SCFAs production. SCFAs, short‐chain fatty acids.

Figure 4

Productions of alcohols, aldehydes, and ketones by 110 Lachnospiraceae strains. (A) Scattered bar chart demonstrating the relative amounts of alcohols (n = 86) produced by 110 strains. (B) Scattered bar chart demonstrating the relative amounts of aldehydes (n = 14) produced by 110 strains. (C) Scattered bar chart demonstrating the relative amounts of ketones (n = 35) produced by 110 strains. And for panels (A)–(C), the relative amounts of each metabolite were represented by the relative percentage of metabolite GC‐MS peak area. GC‐MS, Gas Chromatography–Mass Spectrometry.

Figure 5

Productions of pyrazine and its derivatives by the 110 Lachnospiraceae strains. The scattered bar chart demonstrates the relative amounts of pyrazines produced by 110 strains (represented by the relative percentage of metabolite GC‐MS peak area). GC‐MS, Gas Chromatography–Mass Spectrometry.

Figure 6

Major metabolites produced by Blautia (A) and Lachnospira (B) strains. The heights of bar segments represent relative amounts of metabolites (represented by GC‐MS peak area), and only the top 20 metabolites were shown. GC‐MS, Gas Chromatography–Mass Spectrometry.

Figure 7

Distribution and prevalence of Lachnospiraceae‐derived metabolites in human fecal samples of different cohorts. (A) The Venn diagram demonstrating the coverage of volatile metabolites in different cohort studies by Lachnospiraceae metabolites from this study. Cohort study 1 comprising fecal samples from healthy humans (n = 11). Cohort study 2 comprising fecal samples from nonalcoholic fatty liver disease (NAFLD) cohort (n = 30) and its healthy counterparts (n = 30). (B) Bar charts displaying the prevalent volatile metabolites in fecal samples of healthy humans from Cohort study 1 (violet bars) and the numbers of Lachnospiraceae producers in this study (wine red bars). (C) Bar charts displaying the prevalent volatile metabolites in fecal samples of Cohort study 2 (healthy control n = 30, violet bars; and NAFLD patients n = 30, ochre bars) and the numbers of Lachnospiraceae producers in this study (wine red bars). The red asterisk marked five metabolites that were significantly enriched in NAFLD cohort, and two of which were identified in this study (the Lachnospiraceae producers are shown in the panel).