Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

IMA Fungus, Год журнала: 2020, Номер 11(1)

Опубликована: Июль 10, 2020

True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of based on global richness estimates, with around 3 million predicted species. Compared to plants animals, have simple body plans often morphologically ecologically obscure structures. This poses challenges for accurate precise identifications. Here we provide a conceptual framework identification fungi, encouraging approach integrative (polyphasic) taxonomy species delimitation, i.e. combination genealogy (phylogeny), phenotype (including autecology), reproductive biology (when feasible). allows objective evaluation diagnostic characters, either phenotypic or molecular both. Verification identifications is crucial but neglected. Because clade-specific evolutionary histories, there currently no single tool although DNA barcoding using internal transcribed spacer (ITS) remains first diagnosis, particularly in metabarcoding studies. Secondary barcodes are increasingly implemented groups where ITS does not sufficient precision. Issues pairwise sequence similarity-based OTU clustering discussed, multiple alignment-based phylogenetic approaches subsequent verification recommended as more alternatives. In approaches, trade-off between speed accuracy precision must be carefully considered. Intragenomic variation other markers should properly documented, phylotype diversity necessarily proxy richness. Important strategies improve are: (1) broadly document intraspecific intragenomic markers; (2) substantially expand repositories, focusing undersampled clades missing taxa; (3) curation labels primary repositories increase number sequences verified material; (4) link data digital information voucher specimens including imagery. parallel, technological improvements genome sequencing offer promising alternatives future. Despite prevalence DNA-based fungal taxonomy, phenotype-based remain an important strategy catalog establish initial hypotheses.

Язык: Английский

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Petabase-scale sequence alignment catalyses viral discovery

Nature, Год журнала: 2022, Номер 602(7895), С. 142 - 147

Опубликована: Янв. 26, 2022

Public databases contain a planetary collection of nucleic acid sequences, but their systematic exploration has been inhibited by lack efficient methods for searching this corpus, which (at the time writing) exceeds 20 petabases and is growing exponentially1. Here we developed cloud computing infrastructure, Serratus, to enable ultra-high-throughput sequence alignment at petabase scale. We searched 5.7 million biologically diverse samples (10.2 petabases) hallmark gene RNA-dependent RNA polymerase identified well over 105 novel viruses, thereby expanding number known species roughly an order magnitude. characterized viruses related coronaviruses, hepatitis delta virus huge phages, respectively, analysed environmental reservoirs. To catalyse ongoing revolution viral discovery, established free comprehensive database these data tools. Expanding diversity can reveal evolutionary origins emerging pathogens improve pathogen surveillance anticipation mitigation future pandemics.

Язык: Английский

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Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult

Molecular Biology and Evolution, Год журнала: 2020, Номер 38(5), С. 1777 - 1791

Опубликована: Дек. 3, 2020

Numerous studies covering some aspects of SARS-CoV-2 data analyses are being published on a daily basis, including regularly updated phylogeny nextstrain.org. Here, we review the difficulties inferring reliable phylogenies by example snapshot comprising quality-filtered subset 8,736 out all 16,453 virus sequences available May 5, 2020 from gisaid.org. We find that it is difficult to infer these due large number in conjunction with low mutations. further rooting inferred degree confidence either via bat and pangolin outgroups or applying novel computational methods ingroup does not appear be credible. Finally, an automatic classification current into subclasses using mPTP tool for molecular species delimitation also, as might expected, possible, too closely related. conclude that, although application phylogenetic disentangle evolution spread COVID-19 provides insight, results analyses, particular those conducted under default settings inference tools, well downstream phylogenies, should considered interpreted extreme caution.

Язык: Английский

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Dissecting the contribution of host genetics and the microbiome in complex behaviors

Cell, Год журнала: 2021, Номер 184(7), С. 1740 - 1756.e16

Опубликована: Март 11, 2021

Язык: Английский

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Diverse variola virus (smallpox) strains were widespread in northern Europe in the Viking Age

Science, Год журнала: 2020, Номер 369(6502)

Опубликована: Июль 24, 2020

Viking smallpox diversity Humans have a notable capacity to withstand the ravages of infectious diseases. Smallpox killed millions people but drove Jenner's invention vaccination, which eventually led annihilation this virus, declared in 1980. To investigate history smallpox, Mühlemann et al. obtained high-throughput shotgun sequencing data from 1867 human remains ranging >31,000 150 years ago (see Perspective by Alcamí). Thirteen positive samples emerged, 11 were northern European Age (6th 7th century CE). Although sequences patchy and incomplete, four could be used infer phylogenetic tree. This showed distinct lineages with multiple gene inactivations. The analysis pushes back date earliest variola infection humans ∼1000 reveals existence previously unknown virus clade. Science , issue p. eaaw8977 ; see also 376

Язык: Английский

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Population genomics of post-glacial western Eurasia

Nature, Год журнала: 2024, Номер 625(7994), С. 301 - 311

Опубликована: Янв. 10, 2024

Abstract Western Eurasia witnessed several large-scale human migrations during the Holocene 1–5 . Here, to investigate cross-continental effects of these migrations, we shotgun-sequenced 317 genomes—mainly from Mesolithic and Neolithic periods—from across northern western Eurasia. These were imputed alongside published data obtain diploid genotypes more than 1,600 ancient humans. Our analyses revealed a ‘great divide’ genomic boundary extending Black Sea Baltic. hunter-gatherers highly genetically differentiated east west this zone, effect neolithization was equally disparate. Large-scale ancestry shifts occurred in as farming introduced, including near-total replacement many areas, whereas no substantial happened zone same period. Similarly, relatedness decreased transition onwards, whereas, Urals, remained high until around 4,000 bp , consistent with persistence localized groups hunter-gatherers. The dissolved when Yamnaya-related spread 5,000 resulting second major turnover that reached most parts Europe within 1,000-year span. genetic origin fate Yamnaya have elusive, but show Middle Don region contributed them. later admixed individuals associated Globular Amphora culture before expanding into Europe. Similar turnovers Siberia, where report new ‘Neolithic steppe’ cline spanning Siberian forest steppe Lake Baikal. prehistoric had profound lasting on diversity Eurasian populations.

Язык: Английский

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The influence of carbon dioxide on fermentation products, microbial community, and functional gene in food waste fermentation with uncontrol pH

Environmental Research, Год журнала: 2024, Номер unknown, С. 120645 - 120645

Опубликована: Дек. 1, 2024

Язык: Английский

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Composition and metabolism of microbial communities in soil pores

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Апрель 27, 2024

Abstract Delineation of microbial habitats within the soil matrix and characterization their environments metabolic processes are crucial to understand functioning, yet experimental identification remains persistently limited. We combined single- triple-energy X-ray computed microtomography with pore specific allocation 13 C labeled glucose subsequent stable isotope probing demonstrate how long-term disparities in vegetation history modify spatial distribution patterns particulate organic matter drivers habitats, probe bacterial communities populating such habitats. Here we show striking differences between large (30-150 µm Ø) small (4-10 pores (i) diversity, composition, life-strategies, (ii) responses added substrate, (iii) pathways, (iv) processing fate labile C. propose a habitat classification concept based on biogeochemical mechanisms localization also suggests interventions mitigate environmental consequences agricultural management.

Язык: Английский

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Young versus aged microbiota transplants to germ-free mice: increased short-chain fatty acids and improved cognitive performance

Gut Microbes, Год журнала: 2020, Номер 12(1), С. 1814107 - 1814107

Опубликована: Сен. 8, 2020

Aging is associated with cognitive decline and decreased concentrations of short-chain fatty acids (SCFAs) in the gut. SCFAs are significant that they protective to gut other organs. We tested hypothesis aged microbiome alone sufficient decrease host produce decline. Fecal transplant gavages (FTGs) from (18-20 months) or young (2-3 male C57BL/6 mice into germ-free (N = 11 per group) were initiated at ~3 months age. samples collected behavioral testing was performed over study period. Bacterial community structures relative abundances measured fecal by sequencing bacterial 16S ribosomal RNA gene. Mice microbiomes showed clear differences β diversity 30, 60, 90 d (P .001 for each) after FTGs. The SCFAs, acetate, propionate, butyrate (microbiome effect, P < .01 an microbiome. demonstrated depressive-like behavior, impaired short-term memory, spatial memory 3 following initial FTG as assessed tail suspension .008), novel object recognition .001), Barnes Maze .030) tests, respectively. conclude

Язык: Английский

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Lactobacillus plantarum PS128 alleviates neurodegenerative progression in 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-induced mouse models of Parkinson’s disease

Brain Behavior and Immunity, Год журнала: 2020, Номер 90, С. 26 - 46

Опубликована: Июль 30, 2020

Evidence suggests that the Parkinson's disease (PD) pathogenesis is strongly associated with bidirectional pathways in microbiota-gut-brain axis (MGBA), and psychobiotics may inhibit PD progression. We previously reported novel psychobiotic strain, Lactobacillus plantarum PS128 (PS128), ameliorated abnormal behaviors modulated neurotransmissions dopaminergic rodent models. Here, we report orally administering for 4 weeks significantly alleviated motor deficits, elevation corticosterone, nigrostriatal neuronal death, striatal dopamine reduction 1-methyl-4-phenyl-1,2,3,6-tetrathydropyridine (MPTP)-induced mouse ingestion suppressed glial cell hyperactivation increased norepinephrine neurotrophic factors striatum of PD-model mice. administration also attenuated MPTP-induced oxidative stress neuroinflammation pathway. Fecal analysis showed gut microbiota. L. abundance was along methionine biosynthesis-related microbial modules. family Enterobacteriaceae lipopolysaccharide peptidoglycan modules caused by MPTP. In conclude, deficits neurotoxicity.PS128 supplementation inhibited neurodegenerative processes mice help prevent PD.

Язык: Английский

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