DOI: 10.5061/dryad.z08kprrkj
title: Data from: Cryptic diversity of cellulose-degrading gut bacteria in industrialized humans

description: Humans, like all mammals, depend on the gut microbiome for digestion of
 cellulose, the main component of plant fiber, but evidence for cellulose
 fermentation in the human gut is scarce. We have identified ruminococcal
 species in the gut microbiota of human populations that assemble
 functional multi-enzymatic cellulosome systems capable of degrading plant
 cell wall polysaccharides. One of these species, which is strongly
 associated with humans, likely originated in the ruminant gut and was
 subsequently transferred to the human gut potentially during
 domestication, where it underwent diversification and diet-related
 adaptation through the acquisition of genes from other gut microbes.
 Collectively, these species are abundant and widespread among ancient
 humans, hunter-gatherers, and rural populations, but are extremely rare in
 populations from industrialized societies, suggesting potential
 disappearance in response to the westernized lifestyle.
description: # Cryptic diversity of cellulose-degrading gut bacteria in industrialized
 humans Data sources files
 for all figures and supplementary material Description of the data and
 file structure Data S1 Figure 1B tree.nwk is an unrooted phylogenetic
 tree, computed with the maximum likelihood method, of 62 selected genomes
 and MAGs, using the sequence of the ScaC scaffoldin as a phylotyping
 marker. The file contains the newick format used to create phylogenetic
 tree. Data S2 Figure 1C data.xlsx Genomic dissimilarity computed by Mash
 distance within the novel identified ruminococcal cellulosomal species and
 pairwise comparisons to each other as well as to the ruminal R.
 flavefaciens species and the human species, R. champanellensis. Each
 column represents the mash distances. Data S3 Figure 2A.xlsx, Observed
 collective prevalence of the MAGs for fiber-degrading strains in various
 human, apes and NHP cohorts. Values in columns represents the number of
 positive individuals, and percentages are also given for each host
 category. Data S4 Figure 2Ci.xlsx Distribution of each human cellulosomal
 strain (R. champanellensis,  R. hominiciens, R. ruminiciens and R.
 primaciens) across the sample cohorts. For each genome (column A), samples
 (column B) and host (column C), average fold and number of strains are
 given. Data S5 Figure 2Cii.xlsx, Distribution of the human cellulosomal
 strains among the human- and NHP-positive samples. 1st sheet for each
 genome and host, the number of samples is given (column C) as well as the
 percentage of positive samples (column D), the 2nd sheet includes the
 siginificant indval statistics for each genome group. Data S6 Figure 3A
 host tree.nwk is the newick format used to create phylogenetic host tree
 in Figure 3A, a phylogenetic tree of the mammalian host species. Data S7
 Figure 3A tree.nwk is the newick format used to create phylogenetic tree
 in Figure 3A, a core protein phylogenetic tree illustrating the
 co-speciation hypothesis. Data S8 Figure 3B tree.nwk is the newick format
 used to create phylogenetic tree in Figure 3B, a phylogenetic tree of 197
 concatenated core proteins. Data S9 Figure 4C.xlsx concentration of
 reducing sugars is given for the two enzymes at the different time points.
 Comparative cellulolytic activity of ruminococcal GH5 orthologs of either
 human (R. primaciens) or rumen origin (R. flavefaciens FD-1). Enzyme
 samples were examined using microcrystalline cellulose (Avicel) as the
 substrate at 37°C. Data S10 Figure 5A presence/absence (0 or 1) is giving
 for each MAG and gene clusters (column 1). Analysis (PCA) of the overall
 predicted ORFs of the MAGs. Data S11 Figure 5B.xlsx column A verticality
 values for common genes, column B verticality values for specific genes.
 Rank distribution of verticality values for core proteins across the three
 host types versus host-specific proteins indicates that specific genes are
 likely to be transferred via horizontal gene transfer within a given type
 of host. Data S12 Figure 5C in each column number of GH genes for each
 specific MAG. Analysis of the fibrolytic system [indicating glycoside
 hydrolase (GH) families] of the MAGs, according to their hosts. Data S13
 Figure 5D transcripts expression of fibrolytic genes for the 3 hosts, 3
 individual each. Analysis of the expression of the fibrolytic system, as
 examined by transcriptomic analysis of three fecal samples of the three
 hosts (macaque, human and sheep rumen). Data S14 Figure 5E middle panel
 number of specific genes copies for each specific MAG. The statistically
 significant GH families that statistically distinguish the strains
 associated with the three gut ecosystems as determined by the
 Kruskal-Wallis test p* *&lt;0.05 after FDR correction. Data S15 Figure 5E
 right panel transcripts expression of specific genes for the 3 hosts, 3
 individual each. Statistically significant GH expression (metatranscripts
 in FPKM) between the three types of hosts. Data S16 Figure 5E verticality
 values.xlsx verticality values are given for the indicated genes.
 Verticality values for each of statistically significant GH families. Data
 S17 Supplementary Figure S1.xlsx Prevalence of the fibrolytic strains in
 1989 gut metagenomic samples. Sheet 1 presence is given as 1 in column C
 for a specific genome in column B, host group (column D) and host animal
 (column E) and run (column A). Average fold are given in column E,
 lifestyle in G, country in H, number of strains in the samples in I, and
 host category in J. Sheet 2 is the raw data, sheet 3 is same as sheet 2
 but a filtered coverage at 20% for the covered percent column (column T)
 Data S18 Supplementary Figure S2A  Prevalence and abundance of the
 fibrolytic strains in various human and NHPs gut samples. Prevalence of
 the cellulosomal strains (R. hominiciens, R. ruminiciens, R. primaciens
 and R. flavefaciens) is given for various subsampling read depths (5, 10,
 20, 40 and 60 M). The maximal numbers of individuals in the cohorts are
 given for each host category at 5 M read depths.  Sheet 1 prevalences are
 given in column D for a specific genome (column A) readsubsampling (column
 B), host categories are given in column C. Sheet 2 statistics Chi-square
 test , including pvalue, significance and adj. pvalue are given between
 the specific host categories and genomes. In sheet 4 additional metadata
 for the samples with a coverage above 20 % are given including the
 original study in column A. Data S19 Supplementary Figure S2B.xlsx
 Prevalence of the cellulosomal strains for each host category at 10 M read
 depths. Sheet 1 prevalences are given in column D for a specific genome
 (column A) readsubsampling (column B), host categories are given in column
 C. Additional informations include country of origin (column E), host
 (column F), lifestyle (column G), host catergory (column H), depth (column
 I), host species (column J), host group (column K), additional host
 category (column L). Sheet 2 statistics Chi-square test , including
 pvalue, significance and adj. pvalue are given between the specific host
 categories and genomes. Data S20 Supplementary Figure S2C.xlsx Abundance
 of the cellulosomal strains (R. hominiciens, R. ruminiciens, R. primaciens
 and R. flavefaciens) for each category at 20 M read depths. Sheet 1
 abundances are given in column D for a specific genome (column A)
 readsubsampling (column B), samples are given in column C. Sheet 2
 statistics Chi-square test , including pvalue, significance and adj.
 pvalue are given between the specific host categories and genomes. Data
 S21 Supplementary Figure S3.xlsx Prevalence of the fibrolytic strains in
 NHP gut samples. Prevalence of the cellulosomal strains (R. hominiciens,
 R. ruminiciens, R. primaciens and R. flavefaciens) is given for various
 subsampling read depths (5, 10, 20, 40 and 60 M). Sheet 1 prevalences are
 given in column D for a specific genome (column A) readsubsampling (column
 B), lsamples hosts are given in column C. Sheet 2 statistics Chi-square
 test , including pvalue, significance and adj. pvalue are given between
 the specific hosts and genomes. Data S22 Supplementary Figure S4.xlsx :
 Prevalence of the fibrolytic strains in industrialized countries.
 Prevalence of the cellulosomal strains (R. hominiciens, R. ruminiciens, R.
 primaciens and R. flavefaciens) is given for 10 M read depths. Sheet 1
 prevalences are given in column D for a specific genome (column A)
 readsubsampling (column B), locations of the samples are given in column
 C. Sheet 2 statistics Chi-square test , including pvalue, significance and
 adj. pvalue are given between the specific locations and genomes. Data S23
 Supplementary Figure S5.xlsx Prevalence of the fibrolytic strains in rural
 societies countries. Prevalence of the cellulosomal strains (R.
 hominiciens, R. ruminiciens, R. primaciens and R. flavefaciens) is given
 for 10 M read depths. Sheet 1 prevalences are given in column D for a
 specific genome (column A) readsubsampling (column B), locations of the
 samples are given in column C. Sheet 2 statistics Chi-square test ,
 including pvalue, significance and adj. pvalue are given between the
 specific locations and genomes. Data S24 Supplementary Figure S6.xlsx
 Abundance of the MAGs in their ecosystem. Abundance of each MAG in each
 sample is given Data S25 Supplementary Figure S7.xlsx Prevalence of the
 fibrolytic strains in captive and wild NHPs. Prevalence of the
 cellulosomal strains (R. hominiciens, R. ruminiciens, R. primaciens and R.
 flavefaciens) is given for 10 M read depths in various animals (apes:
 chimpanzees, gorillas, and orangutang, other NHPs: macaques, tamarins,
 baboons, mandrills, capuchins, colobus monkeys, guerezas and geladas, and
 ruminants: cows, sheep, camels, yaks and deer). Sheet 1 number of positive
 (column E) and negative samples (column F) out of total number of samples
 examined (column D) is given for each host group (column A) and genomes
 (column B), lifestyle appears in column C. Sheet 2 statistics Chi-square
 test , including pvalue, significance and adj. pvalue are given for the
 specific host groups and genomes. Data S26 Supplementary Figure S8.xlsx
 Prevalence of the fibrolytic strains in omnivore and folivore NHPs.
 Prevalence of the cellulosomal strains (R. hominiciens, R. ruminiciens, R.
 primaciens and R. flavefaciens) is given for 10 M read depths in various
 NHPs (not including apes that are all omnivores). Sheet 1 prevalence
 (column D) of a specific genome (column A) is given, column B is the
 reading depth and column C the diet of the animal. Sheet 2 statistics
 Pearson's Chi-squared test with Yates' continuity correction and
 p value are given for the 3 genomes examined Data S27 Supplementary Figure
 S9.xlsx Identification of core proteins. Presence/absence (0 or 1) is
 giving for each MAG and gene clusters (column 1) Data S28 Supplementary
 Figure S10 tree.nwk Multilocus sequence analysis of the 30 MAGs. The file
 contains the newick format used to create phylogenetic tree in Figure S11
 Data S29 Supplementary Figure S11.xlsx Comparative cellulolytic activity
 of ruminococcal GH5 orthologs of either human (R. primaciens) or rumen
 origin (R. flavefaciens FD-1). Enzyme samples were examined at various
 concentrations using amorphous cellulose as the substrate at 37°C for 1h
 incubation. Concentration of reducing sugars is given for the two enzymes
 at the different enzyme concentrations Data S30 Supplementary Figure
 S12.xlsx Transcriptomic analysis of R. flavefaciens, R. hominiciens and R.
 primaciens strains. The total gene expression in percentage of the
 specific  MAGs in the three fecal samples of the three hosts (macaque,
 human and sheep rumen) is in sheet 1 overall transcripts for the 3 hosts,
 3 individuals each. In sheet 2, 3 and 4 the number of transcripts (in
 FPKM) of each of the indicated cellulosomal genes in three fecal samples
 from either sheep, human or macaque host. Sheet 2, transcripts for the 3
 sheep individuals for each gene, sheet 3, transcripts for the 3 human
 individuals for each gene, sheet 4, transcripts for the 3 macaque
 individuals for each gene/ Data S31 Supplementary Figure S13.xlsx
 Fibrolytic cellulosomal core enzymes of the 30 MAGs with respect to their
 sample of origin (human-, rumen- and NHPs-assembled MAGs). In each column
 number of GH genes for each specific MAG Data S32 197 phylogenetic
 trees.pdf are the compilations of the 197 phylogenetic tree used for
 evolutionary analysis