Nature Microbiology 1, 16131 (2016); published 8 August ...10.1038... · Supplementary Figure 1....
Transcript of Nature Microbiology 1, 16131 (2016); published 8 August ...10.1038... · Supplementary Figure 1....
NATURE MICROBIOLOGY | www.nature.com/naturemicrobiology 1
Corrigendum: The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiotaIlias Lagkouvardos, Rüdiger Pukall, Birte Abt, Bärbel U. Foesel, Jan P. Meier-Kolthoff, Neeraj Kumar, Anne Bresciani, Inés Martínez, Sarah Just, Caroline Ziegler, Sandrine Brugiroux, Debora Garzetti, Mareike Wenning, Thi P. N. Bui, Jun Wang, Floor Hugenholtz, Caroline M. Plugge, Daniel A. Peterson, Mathias W. Hornef, John F. Baines, Hauke Smidt, Jens Walter, Karsten Kristiansen, Henrik B. Nielsen, Dirk Haller, Jörg Overmann, Bärbel Stecher and Thomas Clavel
Nature Microbiology 1, 16131 (2016); published 8 August 2016; corrected 17 October 2016
In the original version of this paper, several of the bacterial genus and species names were incorrect or incompatible with formal taxo-nomic validation and have had to be modified. The relevant names and descriptions have been amended in all versions of the Article. In addition, Supplementary Figs 3,4 and Supplementary Tables 1,4,5,11 have been replaced.
ARTICLESNATURE MICROBIOLOGY DOI: 10.1038/NMICROBIOL.2016.219
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The Mouse Intestinal Bacterial Collection (miBC)provides host-specific insight into cultured diversity
and functional potential of the gut microbiota
Ilias Lagkouvardos, Rüdiger Pukall, Birte Abt, Bärbel U. Foesel, Jan P. Meier-Kolthoff,
Neeraj Kumar, Anne Bresciani, Inés Martínez, Sarah Just, Caroline Ziegler, Sandrine Brugiroux,
Debora Garzetti, Mareike Wenning, Thi P. N. Bui, Jun Wang, Floor Hugenholtz,
Caroline M. Plugge, Daniel A. Peterson, Mathias W. Hornef, John F. Baines, Hauke Smidt,
Jens Walter, Karsten Kristiansen, Henrik B. Nielsen, Dirk Haller, Jörg Overmann,
Bärbel Stecher and Thomas Clavel
SUPPLEMENTARY INFORMATIONARTICLE NUMBER: 16131 | DOI: 10.1038/NMICROBIOL.2016.131
NATURE MICROBIOLOGY | www.nature.com/naturemicrobiology 1
Families (leaf labels):
Sutterellaceae
CoriobacteriaceaeErysipelotrichaceae
Oscillospiraceae
Lactobacillaceae
Porphyromonadaceae
Lachnospiraceae
Eubacteriaceae
Clostridiaceae
Bacteroidaceae
Pasteurellaceae
NA
Ruminococcaceae
Phyla (outer column):
NA
Proteobacteria
Bacteroidetes
Actinobacteria
Firmicutes
0.01
DSM 26109Parasutterella excrementihominisSutterella parvirubraSutterella wadsworthensis
DSM 28627Pasteurella pneumotropica
Haemophilus aegyptiusHaemophilus pittmaniaeAggregatibacter actinomycetemcomitans
Bacteroides faecichinchillae
Bacteroides caccaeBacteroides xylanivoransBacteroides ovatusDSM 26085Bacteroides acidifaciens
Bacteroides faecis
Bacteroides fragilis
DSM 28989
Barnesiella intestinihominisBarnesiella viscericola
Coprobacter fastidiosus
Paludibacter propionicigenesDysgonomonas capnocytophagoidesProteiniphilum acetatigenes
DSM 29508Enterorhabdus caecimuris
Enterorhabdus mucosicola
Asaccharobacter celatusAdlercreutzia equolifaciens
Clostridium ramosumClostridium spiroforme
Clostridium cocleatum
Catenibacterium mitsuokai
Sharpea azabuensisEggerthia catenaformis
Kandleria vitulina
DSM 29487
DSM 29481Clostridium innocuum
Eubacterium dolichum
Eubacterium limosumPseudoramibacter alactolyticus
Anaerofustis stercorihominisDSM 28593Clostridium butyricum
Ruminococcus bromiiClostridium sporosphaeroidesDSM 26090
Clostridium leptumAnaerotruncus colihominis
Ethanoligenens harbinenseClostridium cellulosi
Pseudoflavonifractor capillosusFlavonifractor plautii
Intestinimonas butyriciproducensDSM 27579Clostridium virideOscillibacter ruminantum
Subdoligranulum variabileFaecalibacterium prausnitzii
Eubacterium ventriosumRoseburia hominis
Clostridium clostridioformeClostridium symbiosum
DSM 29486DSM 28559
Blautia wexleraeDSM 29492
Blautia schinkii
Blautia productaBlautia hydrogenotrophicaBlautia hansenii
Clostridium oroticumEubacterium contortumEubacterium fissicatena
DSM 29489Ruminococcus gnavus
Dorea longicatenaClostridium scindensClostridium hylemonaeDSM 28560
100
100
100100
100
10096
100100
100
100
100100
90100
100
76
64100
100
10092
100
100100
100
100
100
100
100
10094
67100
10098
100100
100
10084
100
100
100
96
10061
9961
100
100
100100
82100
100
100
100
100
6496
100
93
100
10091
94100
100
100100
100100
100100
100
LachnospiraceaeRum
inococcaceaeErysipelotrichaceae
Proposed family clusters
Supplementary Figure 1. Whole proteome-based phylogenomic tree of novel taxa within miBCand closely related species. Affiliation to phyla and families is as in the List of Prokaryotic names withStanding in Nomenclature1. Analysis was based on the latest GBDP algorithm2 and inferred as describedpreviously3 and visualized using iTOL4. Details are given in the Methods section. Type strains are printedin bold face. Label colors represent family affiliation, whereas the outer column denotes the respectivephylum.
Supplementary Figure 2. Distribution of all pairwise 16S rRNA gene sequence similarities.The histograms show the number of comparisons that matched the given percentage identitydisplayed on the x-axis. Analysis included the 15 novel taxa isolated from the mouse gut and62 reference strains. Bars are colored according to the phyla involved in each respective comparison.The figure was visualized using the ggplot package6 for the R statistical framework..
Phyla of reference strainsto which mouse isolateswere compared to:
Actinobacteria
Bacteroidetes
Firmicutes
Proteobacteria
within-mouse comp.
% sequence similarity (16S rRNA gene)
Freq
uenc
y
2 µm2 µm
Frisingicoccus murisDSM 28559
Extibacter murisDSM 28560
Irregularibacter murisDSM 28593
Pasteurella caecimurisDSM 28627
Longicatena caecimuris DSM 29481
10 µm
Cuneatibacter caecimuris DSM 29486
5 µm
2 µm
2 µm
5 µm
Longibaculum muris DSM 29487
5 µm
‘Blautia caecimuris’DSM 29492
2 µm
Enterorhabdus muris DSM 29508
Flintibacter butyricusDSM 27579
Acutalibacter murisDSM 26090
2 µm
2 µm
5 µm
Muricomes intestini DSM 29489
Supplementary Figure 3. Light
microscopic images of novel bacteria
within miBC. The images are
representatives of approximately 20 observed
microscopic fields and three to five recorded
images per strain. Microscopic pictures of
‘Bacteroides caecimuris’ DSM 26085,
‘Turicimonas muris’ DSM 26109, and
‘Muribaculum intestinale’ DSM 28989 will be
published elsewhere (Brugiroux et al.)
0%
40%
80%
0%
40%
80%
Tot. prevalenceD
ietM
ouse geneticsH
ousing lab
‘Acutalibactermuris’
DSM26090T
‘Muribaculumintestinale’DSM28989T
‘Bacteroidescaecimuris’DSM26085T
‘Enterorhabdusmuris’
DSM29508T
‘Flintibacterbutyricus’
DSM27579T
>60 % <60 %
high-fat control
swiss websterSV129SJL-C57BL/6SJLNODC57BL/6BALB/c129S
UGOTUCPHPfizerNIFESDTUBGI (as in Xiao et al., Nat Biotech, 2015)
Supplementary Figure 4. Occurrence of the 5 novel bacteria in miBC that matchedmetagenomic species. Technical details are given in the text. The metagenomic dataset wasobtained from 184 mouse fecal samples originating from 6 housing laboratories and 5 differentproviders5. Original data are provided Supplementary Table 5.
pvalue:0.00106 corrected:0.0046re
lativ
e se
quen
ce a
bund
ance
(%)
F8
F5
F7F6
F2
F3
F1
F4
Number ofpositive samples
1
5
4
6
5
23
37
5
Total
5
5
4
8
5
23
38
5
F8F5 F7F6F2 F3F1 F4
0
5
10
15
20
family S24−7 (’Muribaculaceae’)
Supplementary Figure 5. Relative sequence abundance of family S24-7. Caecal samples collected from 93 mice housed in eight animal facilities (F1-8) were analyzed by high-throughput 16S rRNA genesequencing. The total number of mice per facility and those which were positive for family S24-7(number of positive samples) are indicated below the boxplots, which show median values andinter-quartile ranges. The p-value was obtained using ANOVA and corrected following theBenjamini-Hochberg method.
Supplementary Figure 6. Dendrogram analysis of PFAM profiles. The dendrogram was
calulcated in the R programming environment using the Jaccard method. The heatmap shows
PFAM in a binary presence/absence fashion (blue/white) ranked according to decreasing PFAM
prevalence (from left to right) across all samples (metagenomes and cultivable genome collections).
Core (present in all samples) and isolate-specific PFAM are indicated by the black line and green
arrows, respectively. Corresponding PFAM lists are provided in Supplementary Table 12.
SIHUMI (8 strains)
MIBAC-1 (18 strains)
ASF (8 strains)
Metagenomes (n = 17)
miBC (76 species)
PFAMs
Supplementary Table 1. List of strains included in the mouse intestinal bacterial
collection. This file contains (A) the list of 100 strains in miBC with corresponding
information, including: species name, original strain designation, DSMZ number,
Genbank accession number of 16S rRNA gene sequences, most closely related
species, taxonomy, genome accession number, atmosphere requirement, and origin; (B)
information on the minimal bacterial consortia analyzed in the present study.
Supplementary Table 2. Genome-derived pairwise similarities between all 16S
rRNA gene sequences.
Supplementary Table 3. All pairwise digital DNA:DNA hybridization (dDDH)
estimates with confidence intervals. See the Methods section for details on the
calculation procedure.
Supplementary Table 4. Enzymatic profiles of novel bacterial taxa as assessed
with the suitable API test strips.
Supplementary Table 5. Metagenomic species analysis. The 15 novel bacterial taxa
obtained in the present study were analyzed against the mouse gene catalog5 and
searched for similarity with metagenomic species (MGS). This file contains information
on (A) the number of hits to the gene catalog for each new species; (B) MGS
characteristics for the 5 new taxa with significant hits; and (C) number of fecal samples
positive for each of these 5 taxa across the different mouse categories
Supplementary Table 6. High-throughput 16S rRNA gene sequence analysis:
Metadata and OTU table with normalized relative sequence abundances. A total of
93 mouse caecal samples were analyzed by sequencing V5/6 regions of the 16S rRNA
gene as described in detail in the text. Data were analyzed using IMNGS
(www.imngs.org) with a pipeline developed in-house based on UPARSE7. OTUs
occurring at a relative abundance >0.1 % total reads in at least one sample were kept
for analysis.
Supplementary Table 7. High-throughput 16S rRNA gene sequence analysis: raw
sequence counts.
Supplementary Table 8. Animal facility-specific indicator species as derived by
high-throughput 16S rRNA gene sequence analysis.
Supplementary Table 9. Raw output of the integrated 16S rRNA-based studies
based on IMNGS. The tool is available at www.imngs.org. The nearly full-length 16S
rRNA gene sequences of all 76 species in miBC were used as queries to assess their
occurrence and prevalence in the pool of 51,073 high-throughput 16S rRNA datasets
stored in the Sequence Read Archive (SRA). The present file contains the raw output of
the analysis as delivered by IMNGS, including sequence counts for each miBC species
and SRA samples at the level of 97% sequence identity.
Supplementary Table 10. List of mouse and human fecal metagenomes used in
the present study to assess coverage by the collection of cultured strains and by
minimal bacteriomes.
Supplementary Table 11. Composition of the random sets of miBC-derived strains
used to test the relevance of the data-driven selection MIBAC-1.
Supplementary Table 12. Core and miBC-specific PFAM features.
Supplementary Sequence File. This file contains the partial nucleotide sequences of
all operational taxonomic units from the high-throughput 16S rRNA gene dataset
generated in the present study.
Supplementary references
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available on the Internet. International journal of systematic bacteriology 47, 590-
592 (1997).
2. Meier-Kolthoff JP, Auch AF, Klenk HP, Goker M. Genome sequence-based
species delimitation with confidence intervals and improved distance functions.
BMC bioinformatics 14, 60 (2013).
3. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Highly parallelized inference of
large genome-based phylogenies. In: Concurrency Computation Practice and
Experience (ed^(eds) (2014).
4. Letunic I, Bork P. Interactive Tree Of Life v2: online annotation and display of
phylogenetic trees made easy. Nucleic acids research 39, W475-478 (2011).
5. Xiao L, et al. A catalog of the mouse gut metagenome. Nature biotechnology 33,
1103-1108 (2015).
6. Wickham H. Ggplot2: Elegant Graphics for Data Analysis. Springer (2009).
7. Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon
reads. Nature methods 10, 996-998 (2013).