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...Conor
Meehan
& Rob Beiko
Meet the Lachnospiraceae
Bryant and Small, 1956
fao.org
Wooly Coil+
Meet the Lachnospiraceae
Bacteria
Archaea
Pigeon:
Fir0002/Flagstaffotos (Wikimedia Commons)
Things that are made of cells
Meet the Lachnospiraceae
Firmicutes
Proteobacteria
Domain Bacteria
Actinobacteria
Bacteroidetetetes
Cyanobacteria
Interesting weirdos
(Aquificae, Thermotogae, Nitrospirae,
Syergistetes, Elusimicrobia, TM7, TMZ,
OP6, and so on)
Acidobacteria (maybe)
Meet the Lachnospiraceae
Clostridia
Phylum Firmicutes
(aka, Low-G+C Gram-positives)
Negativicutes
Erysipelotrichia
Thermolithobacteria
Bacilli
Meet the Lachnospiraceae
Clostridiales
Class Clostridia
Natranaerobiales
Thermoanaerobacterales
Halanaerobiales
Bathrobiales
Meet the Lachnospiraceae
Lachnospiraceae
Order Clostridiales
Caldicoprobacteraceae
Catabacteriaceae
Ruminococcaceae
Clostridiaceae
Eubacteriaceae
Gracekellibacteraceae
Peptococcaceae
Peptostreptococcaceae
Peptostreptokleptococcaceae
Lachnospiraceae and the
Gastrointestinal Festival
Lachnospiraceae respond to changing conditions in the gut and rumen
Dorea
(the explorea)
x2
Roseburia
x2
Lachnospira
Lachnospiraceae as
therapeutics?
Blautia
Butyric
acid
Ben Mills,
https://commons.wikimedia.org/
Produced by many (…all?) Lachnospiraceae
- Important energy source. Thanks, microbiome!
- Potential regulator of mucosal gene expression
- Protective against some diseases (e.g. colitis)
- Inhibitor of cancer cell proliferation?
- Suppressor of C. difficile
Taxonomy, phylogeny
(16S and so on)
Function (genomes,
metagenomes)
Ecology (distribution)
http://bighugelabs.com/badge.php
Image: http://ijsb.sgmjournals.org/content/53/1/201/F3.expansion
An identity for
Lachnospiraceae?
Does everyone play the same ecological role (e.g., butyrate production?)
What sort of habitat differentiation exists in the group?
What is their relationship with other groups in the gut and elsewhere?
Searching for
Lachnospiraceae
EMP samples collected from
the QIIME database
GenGIS (http://kiwi.cs.dal.ca/GenGIS)
Abundance in marker-gene
samples
Taxonomy, Phylogeny, Identity
Concatenatedgenes
SSU
Oral Human gut SedimentRumen
Why the disagreement?
• Is 16S wrong?
• Low support values at some nodes
• Is concatenation wrong?
• Most individual gene trees reject the concatenated AND
16S phylogenies
• A mess due to lateral gene transfer?
In search of ecological identity
• Is it butyrate production? Probably NO
Catonella morbi ATCC 51271
Cellulosilyticum lentocellum DSM 5427
Dorea formicigenerans ATCC 27755
Dorea longicatena DSM 13814
Lachnospiraceae bacterium 1_1_57FAA
Lachnospiraceae bacterium 2_1_46FAA
Lachnospiraceae bacterium 2_1_58FAA
Lachnospiraceae bacterium 3_1_46FAA
Lachnospiraceae bacterium 4_1_37FAA
Lachnospiraceae bacterium 5_1_57FAA
Lachnospiraceae bacterium 6_1_63FAA
Lachnospiraceae bacterium 8_1_57FAA
Lachnospiraceae bacterium 9_1_43BFAA
Marvinbryantia formatexigens DSM 14469
Oribacterium sinus F0268
Oribacterium sp. oral taxon 078 str. F0262
Oribacterium sp. oral taxon 108 str. F0425
Coprococcus eutactus ATCC 27759
Butyrivibrio crossotus DSM 2876
Butyrivibrio proteoclasticus B316
Coprococcus comes ATCC 27758
Lachnospiraceae bacterium 1_4_56FAA
Lachnospiraceae bacterium 3_1_57FAA_CT1
Shuttleworthia satelles DSM 14600
Anaerostipes caccae DSM 14662
Anaerostipes sp. 3_2_56FAA
Lachnospiraceae bacterium 5_1_63FAA
Lachnospiraceae oral taxon 107 str. F0167
Roseburia intestinalis L1-82
Roseburia inulinivorans DSM 16841
Showing 1 or 2 of the 3
known pathways
Showing 0 of the 3
known pathways
Butyric acid production:
three different ways,
and
a phylogenetic mess
Roseburia-type butyryl-CoA:acetate CoA-transferase
butyryl-CoA:acetate CoA-transferase
Butyrate kinase
Gut-associated versus everyone else:
2 x sigma factor, 6 x sporulation protein, cell wall
hydrolase (22/1)
3 x sporulation protein (22/0)
Others:
- penicillin-binding protein
- Antimicrobial extrusion protein
- Signal transduction / two-component regulators
- …
In search of ecological identity
II
Spo gene trees are largely consistent with one another
Spo sigma factors present in all genomes
– suggestive of LOSS in oral + rumen genomes
SpoIVA –
sine qua non
The metagenome picture
Lachnospiraceae-associated sporulation
genes in human gut vs. rumen
metagenomes
Mostly mammals: a
Lachnospiraceae Love Story
• Drop acid
• Butyrate production is readily gained and lost (as you
might expect)
• Lose your coat
• The capacity for spore production has been lost several
times
• Leave in someone else’s genes
• LGT has clearly impacted the group in a big way (to be
continued…)
What next?
• Environmental distribution of different Lachno
groups
• Different abundances in healthy vs. diseased?
• Pathway-level analysis of butyrate vs. non-butyrate-
producing strains
• Non-butyrate are enriched for a couple of
“pathogenesis” genes, but nothing compelling yet
• Interesting split in the gut-associated strains
• Detailed profiling of LGT in the group
• New data that we cannot generate ourselves
• Transcriptomics!!
Fin

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Beiko smbe2013-final

  • 2. Meet the Lachnospiraceae Bryant and Small, 1956 fao.org Wooly Coil+
  • 3. Meet the Lachnospiraceae Bacteria Archaea Pigeon: Fir0002/Flagstaffotos (Wikimedia Commons) Things that are made of cells
  • 4. Meet the Lachnospiraceae Firmicutes Proteobacteria Domain Bacteria Actinobacteria Bacteroidetetetes Cyanobacteria Interesting weirdos (Aquificae, Thermotogae, Nitrospirae, Syergistetes, Elusimicrobia, TM7, TMZ, OP6, and so on) Acidobacteria (maybe)
  • 5. Meet the Lachnospiraceae Clostridia Phylum Firmicutes (aka, Low-G+C Gram-positives) Negativicutes Erysipelotrichia Thermolithobacteria Bacilli
  • 6. Meet the Lachnospiraceae Clostridiales Class Clostridia Natranaerobiales Thermoanaerobacterales Halanaerobiales Bathrobiales
  • 7. Meet the Lachnospiraceae Lachnospiraceae Order Clostridiales Caldicoprobacteraceae Catabacteriaceae Ruminococcaceae Clostridiaceae Eubacteriaceae Gracekellibacteraceae Peptococcaceae Peptostreptococcaceae Peptostreptokleptococcaceae
  • 9. Lachnospiraceae respond to changing conditions in the gut and rumen
  • 11. Butyric acid Ben Mills, https://commons.wikimedia.org/ Produced by many (…all?) Lachnospiraceae - Important energy source. Thanks, microbiome! - Potential regulator of mucosal gene expression - Protective against some diseases (e.g. colitis) - Inhibitor of cancer cell proliferation? - Suppressor of C. difficile
  • 12. Taxonomy, phylogeny (16S and so on) Function (genomes, metagenomes) Ecology (distribution) http://bighugelabs.com/badge.php Image: http://ijsb.sgmjournals.org/content/53/1/201/F3.expansion An identity for Lachnospiraceae? Does everyone play the same ecological role (e.g., butyrate production?) What sort of habitat differentiation exists in the group? What is their relationship with other groups in the gut and elsewhere?
  • 14. EMP samples collected from the QIIME database GenGIS (http://kiwi.cs.dal.ca/GenGIS)
  • 18. Why the disagreement? • Is 16S wrong? • Low support values at some nodes • Is concatenation wrong? • Most individual gene trees reject the concatenated AND 16S phylogenies • A mess due to lateral gene transfer?
  • 19. In search of ecological identity • Is it butyrate production? Probably NO Catonella morbi ATCC 51271 Cellulosilyticum lentocellum DSM 5427 Dorea formicigenerans ATCC 27755 Dorea longicatena DSM 13814 Lachnospiraceae bacterium 1_1_57FAA Lachnospiraceae bacterium 2_1_46FAA Lachnospiraceae bacterium 2_1_58FAA Lachnospiraceae bacterium 3_1_46FAA Lachnospiraceae bacterium 4_1_37FAA Lachnospiraceae bacterium 5_1_57FAA Lachnospiraceae bacterium 6_1_63FAA Lachnospiraceae bacterium 8_1_57FAA Lachnospiraceae bacterium 9_1_43BFAA Marvinbryantia formatexigens DSM 14469 Oribacterium sinus F0268 Oribacterium sp. oral taxon 078 str. F0262 Oribacterium sp. oral taxon 108 str. F0425 Coprococcus eutactus ATCC 27759 Butyrivibrio crossotus DSM 2876 Butyrivibrio proteoclasticus B316 Coprococcus comes ATCC 27758 Lachnospiraceae bacterium 1_4_56FAA Lachnospiraceae bacterium 3_1_57FAA_CT1 Shuttleworthia satelles DSM 14600 Anaerostipes caccae DSM 14662 Anaerostipes sp. 3_2_56FAA Lachnospiraceae bacterium 5_1_63FAA Lachnospiraceae oral taxon 107 str. F0167 Roseburia intestinalis L1-82 Roseburia inulinivorans DSM 16841 Showing 1 or 2 of the 3 known pathways Showing 0 of the 3 known pathways
  • 20. Butyric acid production: three different ways, and a phylogenetic mess Roseburia-type butyryl-CoA:acetate CoA-transferase butyryl-CoA:acetate CoA-transferase Butyrate kinase
  • 21. Gut-associated versus everyone else: 2 x sigma factor, 6 x sporulation protein, cell wall hydrolase (22/1) 3 x sporulation protein (22/0) Others: - penicillin-binding protein - Antimicrobial extrusion protein - Signal transduction / two-component regulators - … In search of ecological identity II
  • 22. Spo gene trees are largely consistent with one another Spo sigma factors present in all genomes – suggestive of LOSS in oral + rumen genomes SpoIVA – sine qua non
  • 23. The metagenome picture Lachnospiraceae-associated sporulation genes in human gut vs. rumen metagenomes
  • 24. Mostly mammals: a Lachnospiraceae Love Story • Drop acid • Butyrate production is readily gained and lost (as you might expect) • Lose your coat • The capacity for spore production has been lost several times • Leave in someone else’s genes • LGT has clearly impacted the group in a big way (to be continued…)
  • 25. What next? • Environmental distribution of different Lachno groups • Different abundances in healthy vs. diseased? • Pathway-level analysis of butyrate vs. non-butyrate- producing strains • Non-butyrate are enriched for a couple of “pathogenesis” genes, but nothing compelling yet • Interesting split in the gut-associated strains • Detailed profiling of LGT in the group • New data that we cannot generate ourselves • Transcriptomics!!
  • 26. Fin