Classifying the bacterial gut microbiota of termites and cockroaches: A curated phylogenetic reference database (DictDb).
Recent developments in sequencing technology have given rise to a large number of studies that assess bacterial diversity and community structure in termite and cockroach guts based on large amplicon libraries of 16S rRNA genes. Although these studies have revealed important ecological and evolutionary patterns in the gut microbiota, classification of the short sequence reads is limited by the taxonomic depth and resolution of the reference databases used in the respective studies. Here, we present a curated reference database for accurate taxonomic analysis of the bacterial gut microbiota of dictyopteran insects. The Dictyopteran gut microbiota reference Database (DictDb) is based on the Silva database but was significantly expanded by the addition of clones from 11 mostly unexplored termite and cockroach groups, which increased the inventory of bacterial sequences from dictyopteran guts by 26%. The taxonomic depth and resolution of DictDb was significantly improved by a general revision of the taxonomic guide tree for all important lineages, including a detailed phylogenetic analysis of the Treponema and Alistipes complexes, the Fibrobacteres, and the TG3 phylum. The performance of this first documented version of DictDb (v. 3.0) using the revised taxonomic guide tree in the classification of short-read libraries obtained from termites and cockroaches was highly superior to that of the current Silva and RDP databases. DictDb uses an informative nomenclature that is consistent with the literature also for clades of uncultured bacteria and provides an invaluable tool for anyone exploring the gut community structure of termites and cockroaches.
Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany; LOEWE Center for Synthetic Microbiology (Synmikro), Philipps-Universität Marburg, Marburg, Germany. Electronic address: arammikaelyan@gmail.com.
Aram
A
Mikaelyan
Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
Tim
T
Köhler
Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
Niclas
N
Lampert
Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
Jeffrey
J
Rohland
Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
Hamadi
H
Boga
Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
Katja
K
Meuser
Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany; LOEWE Center for Synthetic Microbiology (Synmikro), Philipps-Universität Marburg, Marburg, Germany. Electronic address: brune@mpi-marburg.mpg.de.
Andreas
A
Brune
D000818:Animals; D001419:Bacteria / Q000145:classification* / Q000235:genetics*; D016000:Cluster Analysis; D003058:Cockroaches / Q000382:microbiology*; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D000069196:Gastrointestinal Microbiome; D059014:High-Throughput Nucleotide Sequencing; D020049:Isoptera / Q000382:microbiology*; D008969:Molecular Sequence Data; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S
16S rRNA; Cockroaches; Deep-sequencing; Gut microbiota; Insects; Termites