The gut microbiomes of 180 species

doi:10.1126/science.abg9095

GSTDTAP > 气候变化

DOI	10.1126/science.abg9095
	The gut microbiomes of 180 species
	Abigail L. Lind; Katherine S. Pollard
	2021-04-16
发表期刊	Science
出版年	2021
英文摘要	Microbial life is ubiquitous in most environments on Earth, including in the gastrointestinal tract of animals. The composition of these collections of microbes, called the microbiota, can differ dramatically between individuals and species. Across the animal tree of life, these microbiotas contain a broad array of microbial diversity. Animal gut microbiota composition is more similar when hosts share diet or genetic ancestry, especially in mammals; the correlation of microbiota composition with genetic ancestry is weaker in fish, reptiles, birds, and invertebrates ([ 1 ][1]–[ 4 ][2]). In many cases, gut microbes contribute to key host processes, including metabolizing specialized dietary compounds ([ 5 ][3]). On page 264 of this issue, Levin et al. ([ 6 ][4]) interrogate the microbes that inhabit the animal gut by sequencing fecal samples from ∼180 wild and captive species across the animal tree of life. Most of the bacterial species and genes they found have not been described before. This massive compendium includes 406 samples from mammals, reptiles, birds, fish, and some invertebrates collected at six different sites globally, with the highest sampling in Israel and Uganda. The animals span a variety of feeding patterns and behavioral traits, although they are predominantly terrestrial vertebrates. The key contribution of Levin et al. is the use of whole-metagenome sequencing, as opposed to the single-gene amplicon sequencing that has yielded much of our current understanding of animal gut microbiome (microbial genomes) composition across diverse groups ([ 5 ][3]). Whole-metagenome sequencing differs from amplicon sequencing in that it involves sequencing all of the DNA present in a sample rather than selecting for a specific piece, as in the case of the 16S ribosomal RNA gene in amplicon sequencing. One major advantage of the whole-metagenome approach is that whole or partial genomes, called metagenome-assembled genomes (MAGs), can be reconstructed by sorting and piecing together the sequencing reads themselves, a process called binning and assembling. Increasingly large numbers of MAGs are being generated from environmental, human, animal, and plant sources, which has revolutionized our understanding of the function, ecology, and evolution of host-associated and environmental microbiotas ([ 7 ][5], [ 8 ][6]). Levin et al. find that most of the reads they sequence from animal microbiomes cannot be mapped to existing reference databases, highlighting the unexplored diversity of animal microbiomes. They use their sequencing reads to assemble more than 5000 MAGs from 1209 bacterial species, of which 75% are uncharacterized. This unexplored microbial diversity in animals stands in contrast to the well-studied human microbiome, which is much better represented by reference databases. The animal microbiota species are distributed across the bacterial tree of life, with the highest enrichment in undescribed species coming from Verrucomicrobia, a phylum found in water, soil, and human intestines but with relatively few cultivated species. Aligning the original sequencing reads back to the MAGs increases the amount of the sequencing library that can be assigned to bacterial genomes from 7 to 21% of reads. That most of the sequences remain unassigned is expected because MAGs do not capture all genomes in a sample. Specifically, they often miss lower-abundance taxa, mobile genetic elements, and organisms with large or complex genomes, including most microbial eukaryotes. Using these assembled genomes, Levin et al. recapitulate findings first noted with amplicon sequencing, including that herbivore microbiomes are more diverse than carnivore microbiomes. By examining the gene content of their MAGs, the authors find that the genetic pathways encoded by the microbiomes of different groups of animals differ based on host diet, body size, and other traits. In a compelling proof-of-concept experiment to demonstrate that new bacterial functions can be discovered in animal microbiomes, the authors experimentally validated bacterial toxin–metabolizing proteases found in the MAGs from carrion-eating griffon vultures ( Gyps fulvus ). These proteases could be useful as antimicrobial compounds, with potential applications that include fighting human food poisoning. The greatest contribution of this study is its rich, systematically generated dataset. It is easy to imagine breakthroughs in areas as diverse as microbial conservation and emerging antibiotic resistance being fueled by discoveries made with these metagenomes. The proteases found in griffon vulture microbiomes are a proof of principle for bioprospecting from wild-animal microbiomes, although it is not clear if this case study should be viewed as exceptional or an expected discovery. This study has just scratched the surface of the hypotheses that can be tested with this dataset. Exciting future directions include questions about how microbiotas help animals degrade toxic plant chemicals, defend from pathogens in food, and extract nutrients from diverse food sources. More broadly, questions remain about what most of the uncharacterized microbes detected by Levin et al. are doing in their hosts and whether they are stably colonizing the animals or transiently passing through their gastrointestinal tracts ([ 2 ][7]). Testing each hypothesis on this massive dataset requires a great deal of computational effort, interpretation, and experimental validation: Each question could be the subject of an entire PhD thesis. Using MAGs limits progress on one of the study's stated aims, which is to enable conservation of medically and ecologically important bacterial strains. Characterizing threatened microbial species will require analyzing the unassembled reads, culturing, or enrichment techniques beyond the whole-metagenome sequencing used in this study. Even for bacteria whose genomes are captured by assembling MAGs, these assemblies are prone to exclude the “accessory” genome, the genes that are variably present across strains. Yet these genes often play roles in adaptations to specific hosts and environments ([ 9 ][8]). For example, antimicrobial resistance, pathogenicity, and energy harvesting are traits frequently encoded by mobile elements or other accessory genes. Reaping all the potential benefits of wild-animal microbiomes will require studying bacterial isolates in most cases. 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领域	气候变化 ; 资源环境
URL	查看原文
引用统计
文献类型	期刊论文
条目标识符	http://119.78.100.173/C666/handle/2XK7JSWQ/322885
专题	气候变化资源环境科学
推荐引用方式 GB/T 7714	Abigail L. Lind,Katherine S. Pollard. The gut microbiomes of 180 species[J]. Science,2021.
APA	Abigail L. Lind,&Katherine S. Pollard.(2021).The gut microbiomes of 180 species.Science.
MLA	Abigail L. Lind,et al."The gut microbiomes of 180 species".Science (2021).