Edward Kirton

Lawrence Berkeley National Laboratory | LBL · Joint Genome Institute

A Correction to this paper has been published: https://doi.org/10.1038/s41587-021-00898-4.

The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and a...

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Sequencing of 16S rRNA gene tags is a popular method for profiling and comparing microbial communities. The protocols and methods used, however, vary considerably with regard to amplification primers, sequencing primers, sequencing technologies; as well as quality filtering and clustering. How results are affected by these choices, and whether data...

Genes associated with elevated oxidative enzyme activities in arid systems have not been well-characterized. To link measured oxidative activities with specific enzymes, we assembled protein-coding reads from the rhizospheres (RHZ) of two aridland grasses. Targeted gene scans for open reading frames, encoding genes potentially involved in lignin mo...

Termites effectively feed on many types of lignocellulose assisted by their gut microbial symbionts. To better understand the microbial decomposition of biomass with varied chemical profiles, it is important to determine whether termites harbor different microbial symbionts with specialized functionalities geared toward different feeding regimens....

Microbial community diversity and phylogenetic composition. (a) Rarefaction curves labeled with the Shannon diversity index (H). (b, c, d, e) Bacterial community composition at the phylum level by 16S rRNA pyrotag (b), by metagenome genes from 38 IMG/M phylogenetic marker COGs (c), and by all genes with function prediction in the metagenomes (d) an...

Natural logarithm of odds ratios of COG categories when comparing the three termite hindgut P3 metagenomes to the average of a total of 149 metagenomes not associated with termites (a) and to the average of all 2456 bacterial genomes (b) in the IMG/M database as publically available in March, 2011. (PDF)

Bioinformatic workflow of metatranscriptome analyses. (PDF)

Transcript distribution among COG categories. (PDF)

Major functions differentially expressed between A. wheeleri and N. corniger metatranscriptomes (PDF)

Hierarchical clustering of metagenomes based on similarities in pfam profiles. Proximity of grouping indicates the relative degree of similarity of samples to each other. The number of genes from each pfam was normalized by the total number of genes from all pfams found in each metagenome to generate the pfam profile. The number in the parenthesis...

A cluster heatmap showing the clustering patterns of lignocellulose-degrading communities based on GH composition (the relative abundance of individual GHs in total GHs, based on gene counts). Only the GHs with the relative abundance ≥2% in any one of these microbiomes were shown in this heatmap. (PDF)

Taxonomic distribution of methyl-accepting chemotaxis protein (MCP) family by MEGAN using Blastp results against the NR database. (PDF)

Metagenome sequencing, assembly and annotation summary (PDF)

Relative abundance of each GH in the four categories of GHs listed above for metagenomes (a) and metatranscriptomes (b). (PDF)

Phylogenetic marker COGs used in phylogenetic distribution (PDF)

Glycoside hydrolase (GH) abundance in metagenomes (PDF)

Estimated average genome size in metagenomes using single-copy phylogenetic markers (PDF)

Metatranscriptome sequencing, assembly, annotation and read mapping summary (PDF)

Major functions differentially represented between A. wheeleri and Nasutitermes spp. Metagenomes (PDF)

Recently, 454 Life Sciences Corporation proposed a new biochemical approach to DNA sequencing (the 454 sequencing). It is based on the pyrosequencing protocol. The 454 sequencing aims to give reliable output at a low cost and in a short time. The produced sequences are shorter than reads produced by classical methods. Our paper proposes a new DNA a...

From the standpoints of both basic research and biotechnology, there is considerable interest in reaching a clearer understanding of the diversity of biological mechanisms employed during lignocellulose degradation. Globally, termites are an extremely successful group of wood-degrading organisms and are therefore important both for their roles in c...

From the standpoints of both basic research and biotechnology, there is considerable interest in reaching a clearer understanding of the diversity of biological mechanisms employed during ligno-cellulose degradation. Globally, termites are an extremely success-ful group of wood-degrading organisms1 and are therefore important both for their roles i...