干旱区生态环境知识资源中心(Arid): MicroNiche: an R package for assessing microbial niche breadth and overlap from amplicon sequencing data

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DOI	10.1093/femsec/fiaa131
	MicroNiche: an R package for assessing microbial niche breadth and overlap from amplicon sequencing data
	Finn, D. R.; Yu, J.; Ilhan, Z. E.; Fernandes, V. M. C.; Penton, C. R.; Krajmalnik-Brown, R.; Garcia-Pichel, F.; Vogel, T. M.
通讯作者	Finn, DR
来源期刊	FEMS MICROBIOLOGY ECOLOGY
ISSN	0168-6496
EISSN	1574-6941
出版年	2020
卷号	96 期号:8
英文摘要	Niche is a fundamental concept in ecology. It integrates the sum of biotic and abiotic environmental requirements that determines a taxon's distribution. Microbiologists currently lack quantitative approaches to address niche-related hypotheses. We tested four approaches for the quantification of niche breadth and overlap of taxa in amplicon sequencing datasets, with the goal of determining generalists, specialists and environmental-dependent distributions of community members. We applied these indices to in silico training datasets first, and then to real human gut and desert biological soil crust (biocrust) case studies, assessing the agreement of the indices with previous findings. Implementation of each approach successfully identified a priori conditions within in silico training data, and we found that by including a limit of quantification based on species rank, one could identify taxa falsely classified as specialists because of their low, sparse counts. Analysis of the human gut study offered quantitative support for Bacilli, Gammaproteobacteria and Fusobacteria specialists enriched after bariatric surgery. We could quantitatively characterise differential niche distributions of cyanobacterial taxa with respect to precipitation gradients in biocrusts. We conclude that these approaches, made publicly available as an R package (MicroNiche), represent useful tools to assess microbial environment-taxon and taxon-taxon relationships in a quantitative manner.
英文关键词	niche theory community ecology proportional similarity index
类型	Article
语种	英语
收录类别	SCI-E
WOS记录号	WOS:000574373300012
WOS关键词	WEIGHT-LOSS ; POPULATION ; DIVERSITY ; ECOLOGY ; KEY
WOS类目	Microbiology
WOS研究方向	Microbiology
来源机构	Arizona State University
资源类型	期刊论文
条目标识符	http://119.78.100.177/qdio/handle/2XILL650/326593
作者单位	[Finn, D. R.] Univ Queensland, Sch Agr & Food Sci, Brisbane, Qld 4072, Australia; [Finn, D. R.; Vogel, T. M.] Univ Lyon, Ecole Cent Lyon, Lab Ampere, Environm Microbial Genom, F-69134 Scully, France; [Yu, J.; Fernandes, V. M. C.; Penton, C. R.] Arizona State Univ, Sch Life Sci, Tempe, AZ 85287 USA; [Yu, J.; Ilhan, Z. E.; Fernandes, V. M. C.; Krajmalnik-Brown, R.; Garcia-Pichel, F.] Arizona State Univ, Ctr Appl & Fundamental Microbi, Tempe, AZ 85287 USA; [Ilhan, Z. E.; Krajmalnik-Brown, R.] Arizona State Univ, Swette Ctr Environm Biotechnol, Tempe, AZ 85287 USA; [Ilhan, Z. E.; Krajmalnik-Brown, R.] Arizona State Univ, Biodesign Inst, Tempe, AZ 85287 USA; [Penton, C. R.] Arizona State Univ, Coll Integrat Sci & Arts, Mesa, AZ 85281 USA
推荐引用方式 GB/T 7714	Finn, D. R.,Yu, J.,Ilhan, Z. E.,et al. MicroNiche: an R package for assessing microbial niche breadth and overlap from amplicon sequencing data[J]. Arizona State University,2020,96(8).
APA	Finn, D. R..,Yu, J..,Ilhan, Z. E..,Fernandes, V. M. C..,Penton, C. R..,...&Vogel, T. M..(2020).MicroNiche: an R package for assessing microbial niche breadth and overlap from amplicon sequencing data.FEMS MICROBIOLOGY ECOLOGY,96(8).
MLA	Finn, D. R.,et al."MicroNiche: an R package for assessing microbial niche breadth and overlap from amplicon sequencing data".FEMS MICROBIOLOGY ECOLOGY 96.8(2020).