CaDAVEr: a metagenome-assembled genome catalog of microbial decomposers across vertebrate environments

TL;DR

This paper introduces a catalog of microbial genomes from soil near decomposing vertebrates to better understand decomposition processes.

Contribution

The study presents 277 new metagenome-assembled genomes from cadaver-associated soils.

Findings

The genomes were recovered from environments associated with vertebrate decomposition.

These genomes can improve understanding of microbial roles in organic matter degradation.

Abstract

Microbial degradation of organic matter is a fundamental Earth process, yet a mechanistic understanding of microbial metabolisms and successional ecology involved in decomposition remains poorly understood. Here, we announce the recovery of 277 cadaver-associated soil metagenome-assembled genomes to enhance our understanding of vertebrate decomposition microbial processes.

Figures

CaDAVEr yields a robust MAG database of microbial decomposers. The taxonomy of the 277 dereplicated MAGs is shown by sequentially colored rings ordered from phylum (P), class (C), order (O), family (F), genus (G), to species (S) assignment. Ring color corresponds to phyla, with the taxonomic assignment denoted in the legend to the left. Gaps at each level represent MAGs that were unclassified at that level of taxonomy (according to GTDB-tk v.2.4.0, r220). The outer ring shows the MAG quality classification, where gray is a medium-quality MAG (completion >50% and contamination <10%), and black is a high-quality MAG (completion >90% and contamination <10%).

Tables

TABLE 1. Quality and genome information of twenty-nine decomposer metagenome-assemble genomes recovered from vertebrate decomposition soils

MAG ID	NCBI accession	Genomesize (bp)	Coverage (×)	Number of scaffolds	N50	Completeness (%)	Contamination (%)	GC	# Predicted genes	Taxonomy (genus)
CMU_advanced.final.11	SAMN35122743	1,738,034	111	186	12,259	89.67	0.88	44.3	1,802	g__Wohlfahrtiimonas
CMU.bins.224	SAMN35122767	1,447,706	78	42	84,618	81.62	0.47	29.9	1,462	g__JASLAT01
CMU.bins.248	SAMN35122772	1,960,261	382	271	8,493	80.27	2.29	40.5	1,759	g__Ignatzschineria
CMU.bins.298	SAMN45170734	1,379,843	3.71502592	260	5,412	71.93	2.18	41.6	1,309	g__Ignatzschineria
CMU.bins.69	SAMN45170740	2,179,327	13.2268609	266	10,819	79.66	6.9	41.2	1,933	g__Ignatzschineria
SHSU_active.final.55	SAMN35122805	2,230,926	31	222	16,150	95.52	0.94	37.6	2,311	g__Savagea
SHSU_active.final.81	SAMN35122806	2,756,840	55	165	23,680	97.42	0	33.7	2,234	g__Bacteroides_E
SHSU_advanced.final.156	SAMN35122812	1,997,474	7	274	9,700	90.58	2.08	37.7	1,899	g__Bacteroides_E
SHSU_advanced.final.35	SAMN35122823	1,258,874	23	248	5,499	74.04	1.14	38.4	1,390	g__Vagococcus_A
SHSU.bins.123	SAMN35122833	3,542,934	63	533	7,822	82.18	4.29	51	3,625	g__Morganella
SHSU.bins.132	SAMN35122835	2,116,720	54	106	25,442	99.71	1.17	45.6	1,961	g__CALZBJ01
SHSU.bins.167	SAMN35122846	2,263,551	21	281	10,811	88.41	1.95	33.6	2,071	g__Bacteroides_E
SHSU.bins.175	SAMN35122849	1,981,783	25	263	9,902	78.09	6.73	41.9	1,749	g__Ignatzschineria
SHSU.bins.195	SAMN35122857	2,596,507	37	254	15,705	88.91	1.17	39.7	2,325	g__Ignatzschineria
SHSU.bins.354	SAMN35122895	1,538,193	46	131	14,935	94.25	0.58	45.4	1,533	g__JAAZCI01
SHSU.bins.365	SAMN35122898	1,752,486	84	45	63,825	97.27	0	44.1	1,629	g__Ignatzschineria
SHSU.bins.50	SAMN35122928	4,056,206	45	729	6,174	51.88	0	58	4,297	g__Klebsiella
SHSU.bins.517	SAMN35122931	1,912,837	24	134	22,260	87.43	3.8	37	1,898	g__Wohlfahrtiimonas
SHSU.bins.531	SAMN35122934	1,451,374	171	291	5,212	62.9	3.31	40.5	1,361	g__Ignatzschineria
SHSU.bins.89	SAMN35122953	1,507,431	46	222	8,450	60.92	4.78	38.7	1,408	g__Ignatzschineria
UTK_active.final.18	SAMN35122955	1,605,292	242	244	7,889	77.55	0.7	47.6	1,679	g__Thiopseudomonas
UTK_active.final.26	SAMN35122956	1,609,873	46	254	7,156	85.83	4.17	46.1	1,799	g__Savagea
UTK.bins.107	SAMN35122961	2,578,716	47	455	6,343	79.81	1.15	40.1	2,608	g__Acinetobacter
UTK.bins.126	SAMN35122964	1,906,363	15	352	5,909	71.72	9.56	40.4	1,925	g__Ignatzschineria
UTK.bins.19	SAMN35122978	2,219,372	43	159	23,955	95.47	1.3	39.5	1,957	g__Bacteroides_E
UTK.bins.42	SAMN35122984	1,863,275	18	142	19,613	93.6	0.39	40	1,884	g__Savagea
UTK.bins.50	SAMN35122986	1,565,609	48	53	63,371	96.34	0.91	36.5	1,510	g__CALAZW01
UTK.bins.71	SAMN35122994	1,322,987	34	287	4,565	64.9	5.35	46	1,491	g__Savagea
UTK.bins.74	SAMN45170746	1,649,164	11.0139592	25	146,272	97.95	0	44.3	1,534	g__JAAZCI01

Full text

ANNOUNCEMENT

Decomposition of organic material, including plants, animals, and their byproducts, is one of the most important ecosystem processes on Earth, requiring complex metabolisms and multi-trophic food webs to efficiently recycle nutrients. Animal tissue decomposition is particularly understudied despite its potential role for innovating agricultural and forensic tools. Microbial communities critical to animal tissue decomposition, also known as the necrobiome (1), lack metagenomic data characterizing this metabolism. Using soils longitudinally collected from 36 terrestrially decomposing human cadavers (n = 21 timepoints per donor) across three U.S. locations (Knoxville, TN; Grand Junction, CO; Huntsville, TX), we present a genomic resource for microbial decomposers of animal tissue (2). Here, we introduce 277 medium- and high-quality metagenome-assembled genomes (MAGs) comprising the CaDAVEr (Catalog of microbial Decomposers Across Vertebrate Environments) database. We highlight 29 taxa previously identified as central members to a co-occurrence network associated with advanced decomposition (Table 1) (2). We have previously shown that these microbes are ubiquitous vertebrate decomposers with insects as a likely vector (2). CaDAVEr members are largely undetected in large databases of host-associated or soil microbial communities, supporting the notion that the necrobiome has an untapped suite of microbial community and functional diversity (2).

Swab samples were collected across decomposition stages from soils adjacent to 36 human cadavers (n = 756). Soil controls (n  =  9), blank controls (n  =  102), and no-template PCR controls (n  =  15) were included. DNA was extracted using the PowerSoil DNA isolation kit 96-htp (MoBio Laboratories) and prepared for shallow metagenomic sequencing. Sequencing (2 × 151 bp) was completed on either an Illumina HiSeq 4000 or an Illumina NovaSeq 6000, resulting in 1,271 Gbp of sequencing and 4,211,654,692 total reads. Adapters were removed, and reads were filtered using Atropos (q = 15, --minimum-length 100, v.1.1.24) (3). Bowtie2 (v.2.2.3) (4) was used to align human sequences against the Genome Reference Consortium Human Build 38 patch release 13, removing all data that matched the reference. Resulting filtered SAM files were converted to FASTQ format with samtools (5) (v.1.3.1) and bedtools (6) (v.2.26.0). Samples with <500 k reads were removed from the analysis as a quality control measure, resulting in a final metagenomics data set of 569 hip-adjacent soil samples, five soil controls, and four no-template controls (N = 575).

Using protocols described previously to maximize genome recovery (7, 8), metagenomes were assembled by geographic site and decomposition stage (MEGAHIT, v.1.2.9, –k-min 41) (9) with assembled scaffolds >2,500 kb binned into MAGs (MetaBAT2, v.2.12.1) (10). Bin quality was assessed by checkM (v.1.1.2) (11), retaining only medium- and high-quality MAGs, which resulted in 1,130 total MAGs (>50% estimated completion and <10% contamination). MAGs were then dereplicated at 99% identity (dRep, v.2.6.2) (12), resulting in 277 MAGs in CaDAVEr, of which 24% are considered high quality (Fig. 1). MAGs were assigned taxonomy via GTDB-tk (v.2.4.0, r220) (13), and genes were annotated using DRAM (v.1.0.0) (14) and were predominantly assigned to the phyla Pseudomonadota (dark red, n = 99), Actinomycetota (dark blue, n = 70), and Bacteroidota (light green, n = 41; Fig. 1). The package default parameters were used unless otherwise specified. Resources of the CaDAVEr database broaden the taxonomic and functional characterization of the vertebrate necrobiome, contributing important phylogenetic and genomic information within decomposition.

CaDAVEr yields a robust MAG database of microbial decomposers. The taxonomy of the 277 dereplicated MAGs is shown by sequentially colored rings ordered from phylum (P), class (C), order (O), family (F), genus (G), to species (S) assignment. Ring color corresponds to phyla, with the taxonomic assignment denoted in the legend to the left. Gaps at each level represent MAGs that were unclassified at that level of taxonomy (according to GTDB-tk v.2.4.0, r220). The outer ring shows the MAG quality classification, where gray is a medium-quality MAG (completion >50% and contamination <10%), and black is a high-quality MAG (completion >90% and contamination <10%).