title: Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores.
abstract: Metagenomic and bioinformatic approaches were used to characterize plant biomass conversion within the foregut microbiome of Australia's "model" marsupial, the Tammar wallaby (Macropus eugenii). Like the termite hindgut and bovine rumen, key enzymes and modular structures characteristic of the "free enzyme" and "cellulosome" paradigms of cellulose solubilization remain either poorly represented or elusive to capture by shotgun sequencing methods. Instead, multigene polysaccharide utilization loci-like systems coupled with genes encoding beta-1,4-endoglucanases and beta-1,4-endoxylanases--which have not been previously encountered in metagenomic datasets--were identified, as were a diverse set of glycoside hydrolases targeting noncellulosic polysaccharides. Furthermore, both rrs gene and other phylogenetic analyses confirmed that unique clades of the Lachnospiraceae, Bacteroidales, and Gammaproteobacteria are predominant in the Tammar foregut microbiome. Nucleotide composition-based sequence binning facilitated the assemblage of more than two megabase pairs of genomic sequence for one of the novel Lachnospiraceae clades (WG-2). These analyses show that WG-2 possesses numerous glycoside hydrolases targeting noncellulosic polysaccharides. These collective data demonstrate that Australian macropods not only harbor unique bacterial lineages underpinning plant biomass conversion, but their repertoire of glycoside hydrolases is distinct from those of the microbiomes of higher termites and the bovine rumen.
authors.affiliation: Commonwealth Scientific and Industrial Research Organization, Division of Livestock Industries, Queensland Bioscience Precinct, St Lucia 4069, Australia.
authors.forename: P B
authors.initials: PB
authors.lastname: Pope
authors.forename: S E
authors.initials: SE
authors.lastname: Denman
authors.forename: M
authors.initials: M
authors.lastname: Jones
authors.forename: S G
authors.initials: SG
authors.lastname: Tringe
authors.forename: K
authors.initials: K
authors.lastname: Barry
authors.forename: S A
authors.initials: SA
authors.lastname: Malfatti
authors.forename: A C
authors.initials: AC
authors.lastname: McHardy
authors.forename: J-F
authors.initials: JF
authors.lastname: Cheng
authors.forename: P
authors.initials: P
authors.lastname: Hugenholtz
authors.forename: C S
authors.initials: CS
authors.lastname: McSweeney
authors.forename: M
authors.initials: M
authors.lastname: Morrison
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics / Q000502:physiology*; D000818:Animals; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000378:metabolism; D044603:Cellulosomes / Q000378:metabolism; D041981:Gastrointestinal Tract / Q000382:microbiology; D006026:Glycoside Hydrolases / Q000145:classification / Q000235:genetics / Q000378:metabolism*; D007614:Macropodidae / Q000235:genetics / Q000382:microbiology / Q000502:physiology*; D054892:Metagenome / Q000235:genetics; D056186:Metagenomics / Q000379:methods; D008969:Molecular Sequence Data; D010802:Phylogeny; D010944:Plants / Q000378:metabolism*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012621:Seasons; D017422:Sequence Analysis, DNA
chemical_list: D012336:RNA, Ribosomal, 16S; D006026:Glycoside Hydrolases