scholarly journals Assessment of Microbial Communities by Graph Partitioning in a Study of Soil Fungi in Two Alpine Meadows

2009 ◽  
Vol 75 (18) ◽  
pp. 5863-5870 ◽  
Author(s):  
L. Zinger ◽  
E. Coissac ◽  
P. Choler ◽  
R. A. Geremia
Keyword(s):  
Microbial Communities ◽  
Graph Partitioning ◽  
Sequence Data ◽  
Large Subunit ◽  
Fungal Communities ◽  
Rrna Gene ◽  
Data Sets ◽  
Alignment Algorithm ◽  
Single Linkage ◽  
Phylogenetic Structure

ABSTRACT Understanding how microbial community structure and diversity respond to environmental conditions is one of the main challenges in environmental microbiology. However, there is often confusion between determining the phylogenetic structure of microbial communities and assessing the distribution and diversity of molecular operational taxonomic units (MOTUs) in these communities. This has led to the use of sequence analysis tools such as multiple alignments and hierarchical clustering that are not adapted to the analysis of large and diverse data sets and not always justified for characterization of MOTUs. Here, we developed an approach combining a pairwise alignment algorithm and graph partitioning by using MCL (Markov clustering) in order to generate discrete groups for nuclear large-subunit rRNA gene and internal transcript spacer 1 sequence data sets obtained from a yearly monitoring study of two spatially close but ecologically contrasting alpine soils (namely, early and late snowmelt locations). We compared MCL with a classical single-linkage method (Ccomps) and showed that MCL reduced bias such as the chaining effect. Using MCL, we characterized fungal communities in early and late snowmelt locations. We found contrasting distributions of MOTUs in the two soils, suggesting that there is a high level of habitat filtering in the assembly of alpine soil fungal communities. However, few MOTUs were specific to one location.

Schistonchus hirtus n. sp. (Nematoda: Aphelenchoididae), an associate of Ficus hirta in China

Nematology ◽  
2010 ◽  
Vol 12 (4) ◽  
pp. 543-556 ◽  
Author(s):  
Yongsan Zeng ◽  
Weimin Ye ◽  
Robin M. Giblin-Davis ◽  
Changhui Li ◽  
Zhijian Du ◽  
...  
Keyword(s):  
Sequence Data ◽  
Large Subunit ◽  
Morphological Characters ◽  
Small Subunit ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Wasp Species ◽  
Dna Sequence Data ◽  
Ficus Hirta ◽  
Large Subunit Rrna

Abstract A nematode recovered from syconia of Ficus hirta from Guangzhou, P. R. China, during a survey of nematode biodiversity from 2007 to 2009, is described herein as Schistonchus hirtus n. sp. and is differentiated by a combination of morphological characters, including excretory pore (EP) located near the metacorpus, a short post-uterine sac (PUS) (0.5 vulval body diam. (VBD) long), rose thorn-shaped spicules, amoeboid sperm, absence of gubernaculum, three pairs of subventral papillae on the male tail, host-Ficus and host-wasp species and DNA sequence data. Morphologically, S. hirtus n. sp. is close to S. centerae, S. altermacrophylla, S. aureus, S. laevigatus and S. virens based upon the length of the PUS (about 0.5 VBD long). However, the relative position of the EP in S. hirtus n. sp. is very different from these species (near metacorpus vs near head). With regard to the EP character, S. hirtus n. sp. is very similar to S. macrophylla, S. guangzhouensis and S. caprifici where the EP is at metacorpus level. However, S. hirtus n. sp. differs from S. macrophylla and S. guangzhouensis by possessing a shorter PUS and smaller spicules, and differs from S. caprifici by a shorter female stylet and smaller spicules. Schistonchus hirtus n. sp. was easily differentiated from other sequenced species by the proportion of parsimony informative changes in the partial small subunit rRNA gene (SSU) and D2/D3 expansion segments of the large subunit rRNA gene (LSU). Phylogenetic analysis with SSU sequences suggests that S. hirtus n. sp. is in a highly supported monophyletic clade with Aphelenchoides and Laimaphelenchus and is polyphyletic to other sequenced Schistonchus species. With LSU sequence data, it forms a clade with S. caprifici and they appear polyphyletic relative to S. guangzhouensis, S. centerae, S. aureus, S. laevigatus and S. virens.

scholarly journals Precise genotyping of circular mobile elements uncovers human associated plasmids with surprisingly recent common ancestors

2021 ◽  
Author(s):  
Nitan Shalon ◽  
David Relman ◽  
Eitan Yaffe
Keyword(s):  
Microbial Communities ◽  
Sequence Data ◽  
Mobile Elements ◽  
Natural Environments ◽  
Data Sets ◽  
Clonal Population ◽  
Data Application ◽  
Population Structures ◽  
Natural Settings ◽  
Common Ancestors

Mobile genetic elements with circular genomes play a key role in the evolution of microbial communities. These circular genomes correspond to cyclic paths in metagenome graphs, and yet, assemblies derived from natural microbial communities produce graphs riddled with spurious cycles, complicating the accurate reconstruction of circular genomes. We present an algorithm that reconstructs true circular genomes based on the identification of so-called ′dominant′ cycles. Our algorithm leverages paired reads to bridge gaps between assembly contigs and scrutinizes cycles through a nucleotide-level analysis, making the approach robust to mis-assembly artifacts. We validated the approach using simulated and reference data. Application of this approach to 32 publicly available DNA shotgun sequence data sets from diverse natural environments led to the reconstruction of hundreds of circular mobile genomes. Clustering revealed 20 clusters of cryptic, prevalent, and abundant plasmids that have clonal population structures with surprisingly recent common ancestors. This work enables the robust study of evolution and spread of mobile elements in natural settings.

scholarly journals Occurrence and Morpho-Molecular Identification of Botryosphaeriales Species from Guizhou Province, China

2021 ◽  
Vol 7 (11) ◽  
pp. 893
Author(s):  
Asha J. Dissanayake ◽  
Ya-Ya Chen ◽  
Ratchadawan Cheewangkoon ◽  
Jian-Kui Liu
Keyword(s):  
Fungal Pathogens ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Elongation Factor ◽  
Morphological Characteristics ◽  
Guizhou Province ◽  
Southwestern China ◽  
Rrna Gene ◽  
Large Subunit Rrna

Botryosphaeriales is an important order of diverse fungal pathogens, saprobes, and endophytes distributed worldwide. Recent studies of Botryosphaeriales in China have discovered a broad range of species, some of which have not been formerly described. In this study, 60 saprobic isolates were obtained from decaying woody hosts in southwestern China. The isolates were compared with other species using morphological characteristics, and available DNA sequence data was used to infer phylogenetic analyses based on the internal transcribed spacer (ITS), large subunit rRNA gene (LSU), and translation elongation factor 1-α (tef) loci. Three novel species were illustrated and described as Botryobambusa guizhouensis, Sardiniella elliptica, and Sphaeropsis guizhouensis, which belong to rarely identified genera within Botryosphaeriaceae. Botryobambusa guizhouensis is the second species identified from the respective monotypic genus. The previously known species were identified as Aplosporella hesperidica, Barriopsis tectonae, Botryosphaeria dothidea, Diplodia mutila, Di. neojuniperi, Di. pseudoseriata, Di. sapinea, Di. seriata, Dothiorella sarmentorum, Do. yunnana, Lasiodiplodia pseudotheobromae, Neofusicoccum parvum, Sardiniella celtidis, Sa. guizhouensis, and Sphaeropsis citrigena. The results of this study indicate that numerous species of Botryosphaeriales are yet to be revealed in southwestern China.

scholarly journals Fluoxetine-induced alteration of murine gut microbial community structure: evidence for a microbial endocrinology-based mechanism of action responsible for fluoxetine-induced side effects

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6199 ◽  
Author(s):  
Mark Lyte ◽  
Karrie M. Daniels ◽  
Stephan Schmitz-Esser
Keyword(s):  
Body Weight ◽  
Weight Gain ◽  
Side Effects ◽  
Gut Microbiota ◽  
Microbial Communities ◽  
Time Course ◽  
Selective Serotonin Reuptake Inhibitors ◽  
Sequence Data ◽  
Rrna Gene ◽  
Dosing Regimen

Background Depression and major depressive disorder affect 25% of the population. First line treatment utilizing selective serotonin reuptake inhibitors (SSRIs) have met with limited success due to well-recognized negative side effects which include weight gain or loss. This inability to control unwanted side effects often result in patients stopping their antidepressant medications. The mechanisms underlying the failure of SSRIs are incompletely understood. Methods Male CF-1 mice (5 weeks of age, N = 10 per group) were per orally administered fluoxetine (20 mg per kg body weight) or diluent daily for 29 days. During this time fecal specimens were collected at three defined time points (0, 15 and 29 days). At the conclusion of the 29-day dosing regimen, animals were subjected to two behavioral assessments. For bacterial identification of the microbiota, 16S rRNA gene sequencing was performed on 60 fecal specimens (three specimens per mouse time course, N = 20 mice) using Illumina MiSeq. Analysis of community sequence data was done using mothur and LEfSe bioinformatic software packages. Results Daily per oral administration of fluoxetine for 29 days to male mice resulted in a significant, time dependent, alteration in microbial communities accompanying changes in body weight. The calculated species richness and diversity indicators of the murine fecal microbial communities were inconsistent and not significantly different between the groups. Among the phylotypes decreased in abundance due to fluoxetine administration were Lactobacillus johnsonii and Bacteroidales S24-7 which belong to phyla associated with regulation of body mass. The observed changes in body weight due to fluoxetine administration mimicked the dramatic shifts in weight gain/loss that has been observed in humans. Further, at the conclusion of the 29-day dosing regimen fluoxetine-dosed animals evidenced a mild anxiogenic-like behavior. Discussion We report that the most widely used antidepressant, fluoxetine, which is an SSRI-type drug, results in the selective depletion of gut microbiota, specifically the Lactobacilli which are involved in the regulation of body weight. Concomitantly, fluoxetine administration increases the abundance of phylotypes related to dysbiosis. Since Lactobacilli have been previously shown to possess a known biogenic amine transporter that regulates the uptake of fluoxetine, it is proposed that a microbial endocrinology-based mechanistic pathway is responsible for the ability of SSRIs to selectively negatively impact beneficial microbiota. The results of this study therefore suggest that the negative clinical side effects due to fluoxetine administration may be due to alterations in gut microbiota. Further, the data also suggests that supplementation of bacterial genera directly affected by fluoxetine administration may prove useful in ameliorating some of the well-known side effects of chronic fluoxetine administration such as weight alterations.

scholarly journals TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution

mSphere ◽  
2018 ◽  
Vol 3 (5) ◽  
Author(s):  
Robin R. Rohwer ◽  
Joshua J. Hamilton ◽  
Ryan J. Newton ◽  
Katherine D. McMahon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Microbial Community Composition ◽  
Taxonomic Resolution ◽  
Rrna Gene ◽  
Data Sets ◽  
Data Set ◽  
Comprehensive Database ◽  
Fine Resolution

ABSTRACT Taxonomy assignment of freshwater microbial communities is limited by the minimally curated phylogenies used for large taxonomy databases. Here we introduce TaxAss, a taxonomy assignment workflow that classifies 16S rRNA gene amplicon data using two taxonomy reference databases: a large comprehensive database and a small ecosystem-specific database rigorously curated by scientists within a field. We applied TaxAss to five different freshwater data sets using the comprehensive SILVA database and the freshwater-specific FreshTrain database. TaxAss increased the percentage of the data set classified compared to using only SILVA, especially at fine-resolution family to species taxon levels, while across the freshwater test data sets classifications increased by as much as 11 to 40% of total reads. A similar increase in classifications was not observed in a control mouse gut data set, which was not expected to contain freshwater bacteria. TaxAss also maintained taxonomic richness compared to using only the FreshTrain across all taxon levels from phylum to species. Without TaxAss, most organisms not represented in the FreshTrain were unclassified, but at fine taxon levels, incorrect classifications became significant. We validated TaxAss using simulated amplicon data derived from full-length clone libraries and found that 96 to 99% of test sequences were correctly classified at fine resolution. TaxAss splits a data set’s sequences into two groups based on their percent identity to reference sequences in the ecosystem-specific database. Sequences with high similarity to sequences in the ecosystem-specific database are classified using that database, and the others are classified using the comprehensive database. TaxAss is free and open source and is available at https://www.github.com/McMahonLab/TaxAss. IMPORTANCE Microbial communities drive ecosystem processes, but microbial community composition analyses using 16S rRNA gene amplicon data sets are limited by the lack of fine-resolution taxonomy classifications. Coarse taxonomic groupings at the phylum, class, and order levels lump ecologically distinct organisms together. To avoid this, many researchers define operational taxonomic units (OTUs) based on clustered sequences, sequence variants, or unique sequences. These fine-resolution groupings are more ecologically relevant, but OTU definitions are data set dependent and cannot be compared between data sets. Microbial ecologists studying freshwater have curated a small, ecosystem-specific taxonomy database to provide consistent and up-to-date terminology. We created TaxAss, a workflow that leverages this database to assign taxonomy. We found that TaxAss improves fine-resolution taxonomic classifications (family, genus, and species). Fine taxonomic groupings are more ecologically relevant, so they provide an alternative to OTU-based analyses that is consistent and comparable between data sets.

Description of Schistonchus microcarpus n. sp. (Nematoda: Aphelenchoididae), an associate of Ficus microcarpa in China

Nematology ◽  
2011 ◽  
Vol 13 (2) ◽  
pp. 221-233 ◽  
Author(s):  
Yongsan Zeng ◽  
Weimin Ye ◽  
Robin Giblin-Davis ◽  
Changhui Li ◽  
Shinian Zhang ◽  
...  
Keyword(s):  
Excretory Pore ◽  
Sequence Data ◽  
Large Subunit ◽  
Small Subunit ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Male Tail ◽  
Mtdna Coi ◽  
Ficus Microcarpa ◽  
Tail Tip

AbstractSchistonchus microcarpus n. sp. was recovered from the syconia of Ficus microcarpa from Shenzhen and Guangzhou, Guangdong Province, China, during a survey of nematode biodiversity from 2007 to 2009. It is characterised by possessing the combined characters of a short post-uterine sac (PUS) (3-11 μm or <0.4 vulval body diam. (VBD) long), excretory pore located just posterior to the head but anterior to the conus level of the stylet, prominent amphids, three pairs of subventral papillae on the male tail (one pair adcloacal, one pair halfway between cloaca and tail terminus, and one pair near tail tip), unique recurved and sickleshaped spicules with finely rounded tip with cucullus, amoeboid sperm, and rounded male tail tip with or without mucron. Schistonchus microcarpus n. sp. is morphologically differentiated from all other described species in this genus by the possession of a spicule with a cucullus on the tip. Schistonchus microcarpus n. sp. was easily differentiated from other sequenced species by the partial small subunit rRNA gene (SSU) and D3 expansion segments of the large subunit rRNA gene (LSU). Phylogenetic analysis with partial SSU sequences suggests that S. microcarpus n. sp. is in a highly supported monophyletic clade with sequenced Schistonchus species except for S. hirtus. Based upon inferences using D3 LSU sequence data, it forms a clade with an undescribed species of Schistonchus ex F. benjamini from Australia and is part of a larger clade of Schistonchus that mostly share the character of an anteriorly placed excretory pore. Sequences of partial mtDNA COI (590 bp) from males of S. microcarpus n. sp. with and without a mucronate tail tip were identical, proving that these two morphotypes are conspecific.

scholarly journals DISTINCT INTESTINAL MICROBIAL COMMUNITIES OF TWO SYMPATRIC ANADROMOUS ARCTIC SALMONIDS AND THE EFFECTS OF MIGRATION AND FEEDING

2020 ◽  
Author(s):  
Geraint Element ◽  
Katja Engel ◽  
Josh Neufeld ◽  
John Casselman ◽  
Peter Van Coeverden de Groot ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Microbial Communities ◽  
Sequence Data ◽  
Salvelinus Alpinus ◽  
Microbial Community Composition ◽  
Arctic Char ◽  
Microbial Consortia ◽  
Rrna Gene ◽  
Lake Whitefish ◽  
Abiotic And Biotic Factors

Although intestinal microbial communities from anadromous Arctic char (Salvelinus alpinus) in Kitikmeot, Nunavut, differ depending on the timing and location of capture, determinants of gut microbiota in other wild Arctic salmonids are largely unknown. Using high-throughput 16S rRNA gene sequence data, we compared intestinal microbiota from Arctic char to those from a related and sympatric salmonid, lake whitefish (Coregonus clupeaformis). Shifts in lake whitefish gut microbial community composition were observed between brackish and freshwaters, similar to impacts of salinity reported previously for Arctic char. Despite these similarities, gut community profiles for the two salmonids differed, whitefish having higher diversities and increased proportions of taxa affiliated with potential pathogens. Geography seemed to have a greater impact on freshwater whitefish gut microbiota than on corresponding Arctic char. Additionally, microbiota diversity was significantly more affected by feeding behavior in whitefish compared to sympatric Arctic char. Since sampled whitefish were at their northern range limits and grew slowly, we speculate that they, and their microbial consortia, could be more vulnerable to certain abiotic and biotic factors than Arctic char, which are well adapted to conditions found in these high latitude environments and have the most northerly distribution of any freshwater fish.

scholarly journals Long-Term Drought and Warming Alter Soil Bacterial and Fungal Communities in an Upland Heathland

Ecosystems ◽  
2021 ◽  
Author(s):  
Fiona M. Seaton ◽  
Sabine Reinsch ◽  
Tim Goodall ◽  
Nicola White ◽  
Davey L. Jones ◽  
...  
Keyword(s):  
Climate Change ◽  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Fungal Communities ◽  
Its2 Region ◽  
Rrna Gene ◽  
Summer Drought ◽  
Soil Microbial ◽  
Soil Bacterial

AbstractThe response of soil microbial communities to a changing climate will impact global biogeochemical cycles, potentially leading to positive and negative feedbacks. However, our understanding of how soil microbial communities respond to climate change and the implications of these changes for future soil function is limited. Here, we assess the response of soil bacterial and fungal communities to long-term experimental climate change in a heathland organo-mineral soil. We analysed microbial communities using Illumina sequencing of the 16S rRNA gene and ITS2 region at two depths, from plots undergoing 4 and 18 years of in situ summer drought or warming. We also assessed the colonisation of Calluna vulgaris roots by ericoid and dark septate endophytic (DSE) fungi using microscopy after 16 years of climate treatment. We found significant changes in both the bacterial and fungal communities in response to drought and warming, likely mediated by changes in soil pH and electrical conductivity. Changes in the microbial communities were more pronounced after a longer period of climate manipulation. Additionally, the subsoil communities of the long-term warmed plots became similar to the topsoil. Ericoid mycorrhizal colonisation decreased with depth while DSEs increased; however, these trends with depth were removed by warming. We largely ascribe the observed changes in microbial communities to shifts in plant cover and subsequent feedback on soil physicochemical properties, especially pH. Our results demonstrate the importance of considering changes in soil microbial responses to climate change across different soil depths and after extended periods of time.

Molecular and morphological characterisation of two reproductively isolated species with mirror-image anatomy (Nematoda: Cephalobidae)

Nematology ◽  
1999 ◽  
Vol 1 (6) ◽  
pp. 591-612 ◽  
Author(s):  
Paul De Ley ◽  
Marie-Anne Felix ◽  
Linda Frisse ◽  
Steven Nadler ◽  
Paul Sternberg ◽  
...  
Keyword(s):  
Sequence Data ◽  
Large Subunit ◽  
Mirror Image ◽  
Valid Species ◽  
Rrna Gene ◽  
Separate Species ◽  
Dna Sequence Data ◽  
Left Handed ◽  
The Right ◽  
Large Subunit Rrna

Abstract Detailed descriptions are given of the amphimictic nematode strains PS1158, PS2052 and PS2160, which are unusual in that they only differ in predominant body handedness. Although these strains are morphologically identical in all other respects, published reproductive data and new DNA sequence data of the D2/D3 region of the large subunit rRNA gene show that they do represent two separate species. On the basis of comparison with type material, the left-handed strains PS1158 and PS2160 are identified as Acrobeloides bodenheimeri, and the right-handed strain PS2052 as A. camberenensis, which is re-instated as a valid species. A. bodenheimeri and its relatives exhibit various types of diagnostic and taxonomic problems at species level, and it is shown that D2/D3 sequence data provide an important new diagnostic tool for addressing these problems. Phylogenetic analysis shows that two right-handed parthenogenetic strains identified as A. maximus represent a third species which is more closely related to A. camberenensis than to A. bodenheimeri. Caracterisation morphologique et moleculaire de deux especes intersteriles de chiralite contraire (Nematoda: Cephalobidae) - Une description detaillee est donnee des souches amphimictiques de nematodes PS1158, PS2052 et PS2160, souches inhabituelles car differant par la chiralite du corps. Bien que ces souches soient morphologiquement identiques sous tout autre rapport, les resultats publies de tests de croisement et de nouvelles donnees concernant la sequence d'ADN de la region D2/D3 du gene de la grosse sous-unite d'ARN ribosomal montrent qu'elles representent en fait deux especes distinctes. Se fondant sur une comparaison avec le materiel type, les souches sinistres PS1158 et PS2160 sont identifiees comme Acrobeloides bodenheimeri et la souche dextre PS2052 comme A. camberenensis, ainsi retabli comme espece valide. A. bodenheimeri et les especes proches posent differents problemes diagnostiques et taxinomiques au niveau specifique, et nous montrons que les donnees de sequence D2/D3 fournissent un nouvel outil diagnostique important pour aborder ces problemes. L'analyse phylogenetique montre que deux souches parthenogenetiques dextres identifiees comme A. maximus representent en fait une troisieme espece, plus proche de A. camberenensis que de A. bodenheimeri.

scholarly journals Metagenomic Analyses: Past and Future Trends

2010 ◽  
Vol 77 (4) ◽  
pp. 1153-1161 ◽  
Author(s):  
Carola Simon ◽  
Rolf Daniel
Keyword(s):  
Microbial Communities ◽  
Sequence Data ◽  
Extreme Environments ◽  
Data Sets ◽  
Metagenomic Dna ◽  
Functional Dynamics ◽  
Dna Libraries ◽  
Water Analyses ◽  
Independent Assessment ◽  
Generation Sequencing

ABSTRACTMetagenomics has revolutionized microbiology by paving the way for a cultivation-independent assessment and exploitation of microbial communities present in complex ecosystems. Metagenomics comprising construction and screening of metagenomic DNA libraries has proven to be a powerful tool to isolate new enzymes and drugs of industrial importance. So far, the majority of the metagenomically exploited habitats comprised temperate environments, such as soil and marine environments. Recently, metagenomes of extreme environments have also been used as sources of novel biocatalysts. The employment of next-generation sequencing techniques for metagenomics resulted in the generation of large sequence data sets derived from various environments, such as soil, the human body, and ocean water. Analyses of these data sets opened a window into the enormous taxonomic and functional diversity of environmental microbial communities. To assess the functional dynamics of microbial communities, metatranscriptomics and metaproteomics have been developed. The combination of DNA-based, mRNA-based, and protein-based analyses of microbial communities present in different environments is a way to elucidate the compositions, functions, and interactions of microbial communities and to link these to environmental processes.

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