. . .Conor

Meehan

& Rob Beiko

Meet the LachnospiraceaeBryant 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

ActinobacteriaBacteroidetetetes

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

CaldicoprobacteraceaeCatabacteriaceae

Ruminococcaceae

ClostridiaceaeEubacteriaceae

GracekellibacteraceaePeptococcaceae

Peptostreptococcaceae

Peptostreptokleptococcaceae

Lachnospiraceae and the Gastrointestinal Festival

Lachnospiraceae respond to changing conditions in the gut and rumen

Dorea(the explorea)

x2

Roseburiax2

Lachnospira

Lachnospiraceae astherapeutics?

Blautia

Butyricacid

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.phpImage: 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

Co

nca

ten

ated

gen

es

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 51271Cellulosilyticum lentocellum DSM 5427Dorea formicigenerans ATCC 27755Dorea longicatena DSM 13814Lachnospiraceae bacterium 1_1_57FAALachnospiraceae bacterium 2_1_46FAALachnospiraceae bacterium 2_1_58FAALachnospiraceae bacterium 3_1_46FAALachnospiraceae bacterium 4_1_37FAALachnospiraceae bacterium 5_1_57FAALachnospiraceae bacterium 6_1_63FAALachnospiraceae bacterium 8_1_57FAALachnospiraceae bacterium 9_1_43BFAAMarvinbryantia formatexigens DSM 14469Oribacterium sinus F0268Oribacterium sp. oral taxon 078 str. F0262Oribacterium sp. oral taxon 108 str. F0425

Coprococcus eutactus ATCC 27759Butyrivibrio crossotus DSM 2876Butyrivibrio proteoclasticus B316Coprococcus comes ATCC 27758Lachnospiraceae bacterium 1_4_56FAALachnospiraceae bacterium 3_1_57FAA_CT1Shuttleworthia satelles DSM 14600Anaerostipes caccae DSM 14662Anaerostipes sp. 3_2_56FAALachnospiraceae bacterium 5_1_63FAALachnospiraceae oral taxon 107 str. F0167Roseburia intestinalis L1-82Roseburia 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 anotherSpo sigma factors present in all genomes– suggestive of LOSS in oral + rumen genomes

SpoIVA –sine qua non

The metagenome picture

Lachnospiraceae-associated sporulationgenes 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 Lachnogroups

• 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