Journal: Cell Reports Medicine

Article Title: Intestinal Lachnospiraceae bacterium -derived propionate inhibits the progression of clear cell renal cell carcinoma

doi: 10.1016/j.xcrm.2025.102410

Figure Lengend Snippet: ccRCC-associated gut dysbiosis correlates with tumor progression (A) Experimental workflow: BALB/c mice were treated with ATB to deplete gut microbiota, followed by 14-day FMT from HVs or ccRCC patients, and subcutaneous inoculation with RENCA cells. (B) Tumor growth kinetics in mice receiving microbiota from HVs or ccRCC patients ( n = 6/group). (C and D) Representative images of excised tumors (C) and tumor weights (D) on day 24 ( n = 6/group). (E) Representative Ki67 immunohistochemistry of tumors from the two groups. Scale bars: 100 μm (overview) and 50 μm (magnified region). (F) Individual tumor growth curves in mice transplanted with microbiota from three HVs (HV1–3) or ccRCC (ccRCC1–3) donors. (G) Shannon index of gut microbial diversity in cohort 2 comparing HV and ccRCC. (H) PCoA based on Bray-Curtis distance of fecal microbiota from HV and ccRCC in cohort 2. (I and J) Relative abundance of bacterial orders (I) and families (J) in fecal samples from HV and ccRCC in cohort 2. (K) Shannon index comparing gut microbial diversity between ARCC and LRCC in cohort 2. (L) Relative abundance of bacterial families in fecal samples from ARCC and LRCC. (M) LDA with effect size analysis identifying differentially enriched taxa between HV and ccRCC. Only taxa with LDA score >3 are shown. (N) Relative abundance of Lachnospiraceae bacterium in fecal samples from HV and ccRCC in cohort 2. (O) ROC analysis based on the fecal abundance of L. bacterium distinguishing HVs from ccRCC patients. Data are presented as mean ± SEM. Statistical significance was determined by two-way ANOVA (B), unpaired two-tailed t test (D), one-way ANOVA (E), and Mann-Whitney test (G and N). ∗ p < 0.05, ∗∗ p < 0.01, and ∗∗∗ p < 0.001. See also , and and .

Article Snippet: Lachnospiraceae bacterium , DSMZ , DSM 24404.

Techniques: Immunohistochemistry, Two Tailed Test, MANN-WHITNEY

Journal: iMeta

Article Title: Potential pitfalls in claiming novel taxa

doi: 10.1002/imt2.70036

Figure Lengend Snippet: Demonstration of the 16S rRNA gene sequence features of Lachnospiraceae extracted by Lin et al. using the Barrnap. (A) Distribution of the extracted Lachnospiraceae 16S rRNA gene sequences. There are 176 genomes with a sequence length shorter than 1300 bp and 11 genomes with a sequence length even shorter than 500 bp. Notice that six genomes have extremely long 16S rRNA gene sequences (>2000 bp), which are longer than the entire 16S rRNA gene (~1500 bp). (B) Histogram categorizing sequences into four length groups (0–500 bp, 500–1300 bp, 1300–2000 bp, and >2000 bp), with frequencies indicated on the y ‐axis.

Article Snippet: Extensively related to the paper of Lin et al. [ ], there were 176 species [ ] and 90 genera of Lachnospiraceae (by December of 2023, https://lpsn.dsmz.de/family/Lachnospiraceae ), and Lin et al. stated only 58 genera in their article [ ].

Techniques: Sequencing

Journal: iMeta

Article Title: Isolation of potentially novel species expands the genomic and functional diversity of Lachnospiraceae

doi: 10.1002/imt2.174

Figure Lengend Snippet: The collection of 1868 Lachnospiraceae cultured genomes. (A) Contribution of 756 newly isolated Lachnospiraceae genomes to the existing valid name genera. Genera represented by the human gut cultured genomes are marked in black, genera without human intestinal culture representation but with genomes from other niches are marked in pink, and genera without any cultured genome are marked in gray. (B) Geographical and niche distribution of the number of genomes retrieved. (C) Phylogenetic tree of the 1868 isolated genomes. The tree was produced from concatenated protein sequences using PhyloPhlAn 3. The clades are colored according to the genome source database (The expanded Cultivated Genome Reference [CGR2] or download). Potentially novel species and type strains are marked in the first layer with red and blue dots, respectively. The second and third layers represent the niches and continents where the genomes were isolated, respectively. The GTDB genus annotation is marked at the last layer and text‐labeled for those with multiple lineages. (D) The Jaccard distance distributions of eight multilineage genera within and between branches. *** p < 0.001 as defined by the Wilcoxon test.

Article Snippet: Previous studies analyzing isolated strains of five genera in the Lachnospiraceae family have revealed high diversity between human‐derived isolates [ ], but Lachnospiraceae contains at least 58 genera and 122 valid‐and‐correct‐name species in The List of Prokaryotic names with Standing in Nomenclature (LPSN, https://lpsn.dsmz.de/ , up to July 2021) [ ].

Techniques: Cell Culture, Isolation, Produced, Labeling

Journal: iMeta

Article Title: Isolation of potentially novel species expands the genomic and functional diversity of Lachnospiraceae

doi: 10.1002/imt2.174

Figure Lengend Snippet: New insights into the genes of Lachnospiraceae . (A) The 1.5 M isolated Lachnospiraceae gene catalog, with parts unique to the genomes of potentially new species highlighted in red. (B) The percentage of human gut Lachnospiraceae genes contributing to the human gut microbiota function. (C) The completeness of each metabolic functional module. A bar represents a module, and all modules can be divided into 10 categories according to their functions.

Article Snippet: Previous studies analyzing isolated strains of five genera in the Lachnospiraceae family have revealed high diversity between human‐derived isolates [ ], but Lachnospiraceae contains at least 58 genera and 122 valid‐and‐correct‐name species in The List of Prokaryotic names with Standing in Nomenclature (LPSN, https://lpsn.dsmz.de/ , up to July 2021) [ ].

Techniques: Isolation, Functional Assay

Journal: iMeta

Article Title: Isolation of potentially novel species expands the genomic and functional diversity of Lachnospiraceae

doi: 10.1002/imt2.174

Figure Lengend Snippet: Pan‐genomic diversity of Lachnospiraceae. (A) The number of genes shared between different genomes. The X‐axis is the proportion of genomes containing common genes in all genomes. (B) Core genome, pan‐genome, genome number, and gene number statistics for 41 species with more than 10 genomes sorted by the number of genomes. (C) Phylogenetic unrooted tree constructed based on single‐nucleotide polymorphisms (SNPs). The tree was produced by Parsnp. Nodes are colored according to the isolation country. Clades are divided based on genetic distance. (D) The density of variations frequency at different genome positions of the four clades. The genomic position is colored according to the mutation type. (E) The presence or absence of genes in the Anaerotignum genus. Genes that are only present in the genome of a specific niche are defined as specific genes.

Article Snippet: Previous studies analyzing isolated strains of five genera in the Lachnospiraceae family have revealed high diversity between human‐derived isolates [ ], but Lachnospiraceae contains at least 58 genera and 122 valid‐and‐correct‐name species in The List of Prokaryotic names with Standing in Nomenclature (LPSN, https://lpsn.dsmz.de/ , up to July 2021) [ ].

Techniques: Construct, Produced, Isolation, Mutagenesis

Journal: iMeta

Article Title: Isolation of potentially novel species expands the genomic and functional diversity of Lachnospiraceae

doi: 10.1002/imt2.174

Figure Lengend Snippet: Functional profile of Lachnospiraceae. (A) Distribution of genes associated with short‐chain fatty acid production in each genome. This phylogenetic tree is consistent with Figure . The two pathways for butyrate production from acetyl‐CoA (the Butyryl‐CoA transferase pathway and Butyrate kinase pathway) are presented in the first and second layers, respectively. The third to fifth layers represent the three pathways from propionyl‐CoA to propionate production. The shade of color indicates the type of genes in the pathway, that is, the integrity of the pathway. The last layer represents the genus, which is consistent with Figure . Thl, thiolase; Hdb, β ‐hydroxybutyryl‐CoA dehydrogenase; Cro, crotonase; Bcd, butyryl‐CoA dehydrogenase; But, butyryl‐CoA:acetate CoA transferase; Ptb, phosphate butyryltransferase; Buk, butyrate kinase; ACSS1_2, acetyl‐CoA synthetase; ACSS3, propionyl‐CoA synthetase; Pct, propionate CoA‐transferase; Acd, acetate‐CoA ligase (ADP‐forming); Pta, phosphate acetyltransferase; PduL, phosphate propanoyltransferase; AckA, acetate kinase; TdcD, propionate kinase. (B) Phylogenetic tree of potentially butyrate‐producing genera. The color of the clade represents the genus, and the first layer represents the niche of the genomes. The heat map is colored according to the presence or absence of genes, corresponding to the genes related to the two pathways shown on the left. ACE, Acetatifactor ; AGA, Agathobacter ; ABU, Anaerobutyricum ; ASA, Anaerosacchriphilus ; AST, Anaerostipes ; BAR, Bariatricus ; BAR, Bariatricus ; BUT, Butyrivibrio ; BUT_A, Butyrivibrio _A; CAT, Catenibacillus ; CLO, Clostridium ; CLO_AP, Clostridium _AP; CLO_Q, Clostridium _Q; COP, Coprococcus ; COP_A, Coprococcus _A; EIS, Eisenbergiella ; ENT, Enterocloster ; EUB_F, Eubacterium _F; EUB_G, Eubacterium _G; EUB_H, Eubacterium _H; EUB_I, Eubacterium _I; EUB_Q, Eubacterium _Q; FRI, Frisingicoccus ; KIN, Kineothrix ; LACA, Lachnoanaerobaculum ; LACB, Lachnobacterium ; LAC, Lachnoclostridium ; LAC_A, Lachnoclostridium _A; LAC_B, Lachnoclostridium _B; LACR, Lacrimispora ; MED, Mediterraneibacter _A; PAR, Parasporobacterium ; PSE, Pseudobutyrivibrio ; ROS, Roseburia ; SHU, Shuttleworthia ; ATO, Stomatobaculum ; WEI, Weimeria . (C) Network of the relationship between genera and known secondary metabolites. Genera are represented by dots of their corresponding colors, secondary metabolites are represented by black dots, and the size of the dots is related to the number. (D) Heatmap of sporulation gene distribution.

Article Snippet: Previous studies analyzing isolated strains of five genera in the Lachnospiraceae family have revealed high diversity between human‐derived isolates [ ], but Lachnospiraceae contains at least 58 genera and 122 valid‐and‐correct‐name species in The List of Prokaryotic names with Standing in Nomenclature (LPSN, https://lpsn.dsmz.de/ , up to July 2021) [ ].

Techniques: Functional Assay