Research

19 pages, 2201 KiB

Open AccessArticle

Considerations on the Identity and Diversity of Organisms Affiliated with Sphingobacterium multivorum—Proposal for a New Species, Sphingobacterium paramultivorum

by Yanfang Wang, Jolanda K. Brons and Jan Dirk van Elsas

Microorganisms 2021, 9(10), 2057; https://doi.org/10.3390/microorganisms9102057 - 29 Sep 2021

Cited by 1 | Viewed by 1642

Abstract

Plant biomass offers great potential as a sustainable resource, and microbial consortia are primordial in its bioconversion. The wheat-straw-biodegradative bacterial strain w15 has drawn much attention as a result of its biodegradative potential and superior degradation performance in bacterial-fungal consortia. Strain w15 was [...] Read more.

Plant biomass offers great potential as a sustainable resource, and microbial consortia are primordial in its bioconversion. The wheat-straw-biodegradative bacterial strain w15 has drawn much attention as a result of its biodegradative potential and superior degradation performance in bacterial-fungal consortia. Strain w15 was originally assigned to the species Sphingobacterium multivorum based on its 16S ribosomal RNA (rRNA) gene sequence. A closer examination of this taxonomic placement revealed that the sequence used has 98.9% identity with the ‘divergent’ 16S rRNA gene sequence of S. multivorum NCTC 11343^T, yet lower relatedness with the canonical 16S rRNA sequence. A specific region of the gene, located between positions 186 and 210, was found to be highly variable and determinative for the divergence. To solve the identity of strain w15, genome metrics and analyses of ecophysiological niches were undertaken on a selection of strains assigned to S. multivorum and related species. These analyses separated all strains into three clusters, with strain w15, together with strain BIGb0170, constituting a separate radiation, next to S. multivorum and S. siyangense. Moreover, the strains denoted FDAARGOS 1141 and 1142 were placed inside S. siyangense. We propose the renaming of strains w15 and BIGb0170 as members of the novel species, coined Sphingobacterium paramultivorum. Full article

(This article belongs to the Special Issue Microbial Species Concepts from Theory to Application: A Convergence Study)

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19 pages, 3623 KiB

Open AccessArticle

Single Strain High-Depth NGS Reveals High rDNA (ITS-LSU) Variability in the Four Prevalent Pathogenic Species of the Genus Candida

by Claudia Colabella, Debora Casagrande Pierantoni, Laura Corte, Luca Roscini, Angela Conti, Matteo Bassetti, Carlo Tascini, Vincent Robert and Gianluigi Cardinali

Microorganisms 2021, 9(2), 302; https://doi.org/10.3390/microorganisms9020302 - 02 Feb 2021

Cited by 8 | Viewed by 1916

Abstract

Ribosomal RNA in fungi is encoded by a series of genes and spacers included in a large operon present in 100 tandem repeats, normally in a single locus. The multigene nature of this locus was somehow masked by Sanger sequencing, which produces a [...] Read more.

Ribosomal RNA in fungi is encoded by a series of genes and spacers included in a large operon present in 100 tandem repeats, normally in a single locus. The multigene nature of this locus was somehow masked by Sanger sequencing, which produces a single sequence reporting the prevalent nucleotide of each site. The introduction of next generation sequencing led to deeper knowledge of the individual sequences (reads) and therefore of the variants between the same DNA sequences located in different tandem repeats. In this framework, NGS sequencing of the rDNA region was used to elucidate the extent of intra- and inter-genomic variation at both the strain and species level. Specifically, the use of an innovative NGS technique allowed the high-throughput high-depth sequencing of the ITS1-LSU D1/D2 amplicons of 252 strains belonging to four opportunistic yeast species of the genus Candida. Results showed the presence of a large extent of variability among strains and species. These variants were differently distributed throughout the analyzed regions with a higher concentration within the Internally Transcribed Spacer (ITS) region, suggesting that concerted evolution was not able to totally homogenize these sequences. Both the internal variability and the SNPs between strain can be used for a deep typing of the strains and to study their ecology. Full article

(This article belongs to the Special Issue Microbial Species Concepts from Theory to Application: A Convergence Study)

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19 pages, 4018 KiB

Open AccessArticle

What Is the Best Lens? Comparing the Resolution Power of Genome-Derived Markers and Standard Barcodes

by Angela Conti, Laura Corte, Debora Casagrande Pierantoni, Vincent Robert and Gianluigi Cardinali

Microorganisms 2021, 9(2), 299; https://doi.org/10.3390/microorganisms9020299 - 02 Feb 2021

Cited by 4 | Viewed by 1759

Abstract

Fungal species delimitation was traditionally carried out with multicopy ribosomal RNA (rRNA) genes, principally for their ease of amplification. Since the efficacy of these markers has been questioned, single-copy protein-encoding genes have been proposed alone or in combination for Multi-Locus Sequence Typing (MLST). [...] Read more.

Fungal species delimitation was traditionally carried out with multicopy ribosomal RNA (rRNA) genes, principally for their ease of amplification. Since the efficacy of these markers has been questioned, single-copy protein-encoding genes have been proposed alone or in combination for Multi-Locus Sequence Typing (MLST). In this context, the role of the many sequences obtained with Next-Generation Sequencing (NGS) techniques, in both genomics and metagenomics, further pushes toward an analysis of the efficacy of NGS-derived markers and of the metrics to evaluate the marker efficacy in discriminating fungal species. This paper aims at proposing MeTRe (Mean Taxonomic Resolution), a novel index that could be used both for measuring marker efficacy and for assessing the actual resolution (i.e., the level of separation) between species obtained with different markers or their combinations. In this paper, we described and then employed this index to compare the efficacy of two rRNAs and four single-copy markers obtained from public databases as both an amplicon-based approach and genome-derived sequences. Two different groups of species were used, one with a pathogenic species of Candida that was characterized by relatively well-separated taxa, whereas the other, comprising some relevant species of the sensu stricto group of the genus Saccharomyces, included close species and interspecific hybrids. The results showed the ability of MeTRe to evaluate marker efficacy in general and genome-derived markers specifically. Full article

(This article belongs to the Special Issue Microbial Species Concepts from Theory to Application: A Convergence Study)

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20 pages, 6311 KiB

Open AccessArticle

Homoplasy as an Auxiliary Criterion for Species Delimitation

by Angela Conti, Debora Casagrande Pierantoni, Vincent Robert, Gianluigi Cardinali and Laura Corte

Microorganisms 2021, 9(2), 273; https://doi.org/10.3390/microorganisms9020273 - 28 Jan 2021

Cited by 2 | Viewed by 2325

Abstract

Homoplasy is a sort of noise in phylogenetic reconstructions, due to the accumulation of backmutations, convergent evolution and horizontal gene transfer (HGT), which is considered the major trigger of homoplasy in microorganism for its massive presence. It is also known that homoplasy increases [...] Read more.

Homoplasy is a sort of noise in phylogenetic reconstructions, due to the accumulation of backmutations, convergent evolution and horizontal gene transfer (HGT), which is considered the major trigger of homoplasy in microorganism for its massive presence. It is also known that homoplasy increases with the complexity of the tree with both real and simulated data. In this paper, we analyzed the variation of homoplasy with the two widely used taxonomic markers ITS and LSU in four taxonomic models characterized by differences in the intra-specific distances. An algorithm (HomoDist) was developed to analyze the homoplasy index (HI) variation upon addition of a single element (strain or species) in increasing distance from a starting element. This algorithm allows to follow changes of the consistency index (CI), complementary to the HI, with the increase of the number of taxa and with the increase of the distance among elements. Results show that homoplasy increases—as expected—with the number of taxa, but also as a function of the overall distance among species, often with an almost linear relationship between distance and HI. No HI change was observed in trees with few taxa spanning through short distances, indicating that this noise is not prohibitive in this context, although the analysis of the ratio between HI and distance can be recommended as a criterion for tree acceptance. The absence of large changes of the HI within the species, and its increase when new species are added by HomoDist, suggest that homoplasy variation can be used as an auxiliary test in distance-based species delimitation with any type of marker. Full article

(This article belongs to the Special Issue Microbial Species Concepts from Theory to Application: A Convergence Study)

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25 pages, 5044 KiB

Open AccessArticle

The Taxon Hypothesis Paradigm—On the Unambiguous Detection and Communication of Taxa

by Urmas Kõljalg, Henrik R. Nilsson, Dmitry Schigel, Leho Tedersoo, Karl-Henrik Larsson, Tom W. May, Andy F. S. Taylor, Thomas Stjernegaard Jeppesen, Tobias Guldberg Frøslev, Björn D. Lindahl, Kadri Põldmaa, Irja Saar, Ave Suija, Anton Savchenko, Iryna Yatsiuk, Kristjan Adojaan, Filipp Ivanov, Timo Piirmann, Raivo Pöhönen, Allan Zirk and Kessy Abarenkov Show full author list Hide full author list

Microorganisms 2020, 8(12), 1910; https://doi.org/10.3390/microorganisms8121910 - 30 Nov 2020

Cited by 106 | Viewed by 6675

Abstract

Here, we describe the taxon hypothesis (TH) paradigm, which covers the construction, identification, and communication of taxa as datasets. Defining taxa as datasets of individuals and their traits will make taxon identification and most importantly communication of taxa precise and reproducible. This will [...] Read more.

Here, we describe the taxon hypothesis (TH) paradigm, which covers the construction, identification, and communication of taxa as datasets. Defining taxa as datasets of individuals and their traits will make taxon identification and most importantly communication of taxa precise and reproducible. This will allow datasets with standardized and atomized traits to be used digitally in identification pipelines and communicated through persistent identifiers. Such datasets are particularly useful in the context of formally undescribed or even physically undiscovered species if data such as sequences from samples of environmental DNA (eDNA) are available. Implementing the TH paradigm will to some extent remove the impediment to hastily discover and formally describe all extant species in that the TH paradigm allows discovery and communication of new species and other taxa also in the absence of formal descriptions. The TH datasets can be connected to a taxonomic backbone providing access to the vast information associated with the tree of life. In parallel to the description of the TH paradigm, we demonstrate how it is implemented in the UNITE digital taxon communication system. UNITE TH datasets include rich data on individuals and their rDNA ITS sequences. These datasets are equipped with digital object identifiers (DOI) that serve to fix their identity in our communication. All datasets are also connected to a GBIF taxonomic backbone. Researchers processing their eDNA samples using UNITE datasets will, thus, be able to publish their findings as taxon occurrences in the GBIF data portal. UNITE species hypothesis (species level THs) datasets are increasingly utilized in taxon identification pipelines and even formally undescribed species can be identified and communicated by using UNITE. The TH paradigm seeks to achieve unambiguous, unique, and traceable communication of taxa and their properties at any level of the tree of life. It offers a rapid way to discover and communicate undescribed species in identification pipelines and data portals before they are lost to the sixth mass extinction. Full article

(This article belongs to the Special Issue Microbial Species Concepts from Theory to Application: A Convergence Study)

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19 pages, 2919 KiB

Open AccessArticle

Reanalysis of Lactobacillus paracasei Lbs2 Strain and Large-Scale Comparative Genomics Places Many Strains into Their Correct Taxonomic Position

by Samrat Ghosh, Aditya Narayan Sarangi, Mayuri Mukherjee, Swati Bhowmick and Sucheta Tripathy

Microorganisms 2019, 7(11), 487; https://doi.org/10.3390/microorganisms7110487 - 25 Oct 2019

Cited by 13 | Viewed by 4313

Abstract

Lactobacillus paracasei are diverse Gram-positive bacteria that are very closely related to Lactobacillus casei, belonging to the Lactobacillus casei group. Due to extreme genome similarities between L. casei and L. paracasei, many strains have been cross placed in the other group. We [...] Read more.

Lactobacillus paracasei are diverse Gram-positive bacteria that are very closely related to Lactobacillus casei, belonging to the Lactobacillus casei group. Due to extreme genome similarities between L. casei and L. paracasei, many strains have been cross placed in the other group. We had earlier sequenced and analyzed the genome of Lactobacillus paracasei Lbs2, but mistakenly identified it as L. casei. We re-analyzed Lbs2 reads into a 2.5 MB genome that is 91.28% complete with 0.8% contamination, which is now suitably placed under L. paracasei based on Average Nucleotide Identity and Average Amino Acid Identity. We took 74 sequenced genomes of L. paracasei from GenBank with assembly sizes ranging from 2.3 to 3.3 MB and genome completeness between 88% and 100% for comparison. The pan-genome of 75 L. paracasei strains hold 15,945 gene families (21,5232 genes), while the core genome contained about 8.4% of the total genes (243 gene families with 18,225 genes) of pan-genome. Phylogenomic analysis based on core gene families revealed that the Lbs2 strain has a closer relationship with L. paracasei subsp. tolerans DSM20258. Finally, the in-silico analysis of the L. paracasei Lbs2 genome revealed an important pathway that could underpin the production of thiamin, which may contribute to the host energy metabolism. Full article

(This article belongs to the Special Issue Microbial Species Concepts from Theory to Application: A Convergence Study)

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Review

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14 pages, 1339 KiB

Open AccessReview

Should Networks Supplant Tree Building?

by Rob DeSalle and Margaret Riley

Microorganisms 2020, 8(8), 1179; https://doi.org/10.3390/microorganisms8081179 - 03 Aug 2020

Cited by 5 | Viewed by 2583

Abstract

Recent studies suggested that network methods should supplant tree building as the basis of genealogical analysis. This proposition is based upon two arguments. First is the observation that bacterial and archaeal lineages experience processes oppositional to bifurcation and hence the representation of the [...] Read more.

Recent studies suggested that network methods should supplant tree building as the basis of genealogical analysis. This proposition is based upon two arguments. First is the observation that bacterial and archaeal lineages experience processes oppositional to bifurcation and hence the representation of the evolutionary process in a tree like structure is illogical. Second is the argument tree building approaches are circular—you ask for a tree and you get one, which pins a verificationist label on tree building that, if correct, should be the end of phylogenetic analysis as we currently know it. In this review, we examine these questions and suggest that rumors of the death of the bacterial tree of life are exaggerated at best. Full article

(This article belongs to the Special Issue Microbial Species Concepts from Theory to Application: A Convergence Study)

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Other

Jump to: Research, Review

10 pages, 2177 KiB

Open AccessPerspective

On a Non-Discrete Concept of Prokaryotic Species

by Juan M. Gonzalez, Elena Puerta-Fernández, Margarida M. Santana and Bhagwan Rekadwad

Microorganisms 2020, 8(11), 1723; https://doi.org/10.3390/microorganisms8111723 - 04 Nov 2020

Cited by 5 | Viewed by 2883

Abstract

The taxonomic concept of species has received continuous attention. A microbial species as a discrete box contains a limited number of highly similar microorganisms assigned to that taxon, following a polyphasic approach. In the 21st Century, with the advancements of sequencing technologies and [...] Read more.

The taxonomic concept of species has received continuous attention. A microbial species as a discrete box contains a limited number of highly similar microorganisms assigned to that taxon, following a polyphasic approach. In the 21st Century, with the advancements of sequencing technologies and genomics, the existence of a huge prokaryotic diversity has become well known. At present, the prokaryotic species might no longer have to be understood as discrete values (such as 1 or 2, by homology to Natural numbers); rather, it is expected that some microorganisms could be potentially distributed (according to their genome features and phenotypes) in between others (such as decimal numbers between 1 and 2; real numbers). We propose a continuous species concept for microorganisms, which adapts to the current knowledge on the huge diversity, variability and heterogeneity existing among bacteria and archaea. Likely, this concept could be extended to eukaryotic microorganisms. The continuous species concept considers a species to be delimited by the distance between a range of variable features following a Gaussian-type distribution around a reference organism (i.e., its type strain). Some potential pros and cons of a continuous concept are commented on, offering novel perspectives on our understanding of the highly diversified prokaryotic world, thus promoting discussion and further investigation in the field. Full article

(This article belongs to the Special Issue Microbial Species Concepts from Theory to Application: A Convergence Study)

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