Robust expansion of phylogeny for fast-growing genome sequence data

Massive sequencing of SARS-CoV-2 genomes has led to a great demand for adding new samples to a reference phylogeny instead of building the tree from scratch. To address such challenge, we proposed an algorithm 'TIPars' by integrating parsimony analysis with pre-computed ancestral sequences. Compared to four state-of-the-art methods on four benchmark datasets (SARS-CoV-2, Influenza virus, Newcastle disease virus and 16S rRNA genes), TIPars achieved the best performance in most tests. It took only 21 seconds to insert 100 SARS-CoV-2 genomes to a 100k-taxa reference tree using near 1.4 gigabytes of memory. Its efficient and accurate phylogenetic placements and incrementation for phylogenies with highly similar and divergent sequences suggest that it will be useful in a wide range of studies including pathogen molecular epidemiology, microbiome diversity and systematics.

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Investigating the amphiatlantic status of Facelina bostoniensis (Couthouy, 1838) (Nudibranchia: Aeolidida)

Journal of Molluscan Studies ◽

10.1093/mollus/eyz034 ◽

2020 ◽

Vol 86 (1) ◽

pp. 64-71

Author(s):

Leila Carmona

Keyword(s):

Mediterranean Sea ◽

Sequence Data ◽

Phylogenetic Analyses ◽

16S Rrna Genes ◽

Rrna Genes ◽

Mitochondrial Cytochrome ◽

Molecular Systematic ◽

Dna Sequence Data ◽

Eastern Atlantic Ocean ◽

The Mediterranean

ABSTRACT The aeolid species Facelina bostoniensis (Couthouy, 1838) was originally described from Massachusetts and was later reported from the Eastern Atlantic Ocean and the Mediterranean Sea. So far, no molecular systematic study of its amphiatlantic status has been carried out. Phylogenetic analyses (maximum likelihood and Bayesian) of DNA sequence data for the mitochondrial cytochrome c oxidase subunit I and 16S rRNA genes confirm the amphiatlantic status of F. bostoniensis. My findings show that this species is restricted to the Atlantic realm and that the species recorded from the Mediterranean is not F. bostoniensis but F. vicina (Bergh, 1882). It is hypothesized that previous records of F. bostoniensis from the Mediterranean Sea were actually misidentifications of F. vicina.

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Molecular identification ofSarcocystisspp. helped to define the origin of green pythons (Morelia viridis) confiscated in Germany

Parasitology ◽

10.1017/s0031182013001960 ◽

2013 ◽

Vol 141 (5) ◽

pp. 646-651 ◽

Cited By ~ 9

Author(s):

GASTÓN MORÉ ◽

NIKOLA PANTCHEV ◽

DALAND C. HERRMANN ◽

MAJDA GLOBOKAR VRHOVEC ◽

SABINE ÖFNER ◽

...

Keyword(s):

18S Rrna ◽

Sequence Data ◽

18S Rrna Gene ◽

Rrna Genes ◽

Rrna Gene ◽

Intermediate Hosts ◽

Apicomplexan Parasites ◽

Large Numbers ◽

Wide Range ◽

18S Rrna Genes

SUMMARYSarcocystisspp. represent apicomplexan parasites. They usually have a heteroxenous life cycle. Around 200 species have been described, affecting a wide range of animals worldwide, including reptiles. In recent years, large numbers of reptiles have been imported into Europe as pets and, as a consequence, animal welfare and species protection issues emerged. A sample of pooled feces from four confiscated green pythons (Morelia viridis) containingSarcocystisspp. sporocysts was investigated. These snakes were imported for the pet trade and declared as being captive-bred. Full length 18S rRNA genes were amplified, cloned into plasmids and sequenced. Two differentSarcocystisspp. sequences were identified and registered asSarcocystissp. fromM. viridisin GenBank. Both showed a 95–97% sequence identity with the 18S rRNA gene ofSarcocystis singaporensis.Phylogenetic analysis positioned these sequences together with otherSarcocystisspp. from snakes and rodents as definitive and intermediate hosts (IH), respectively. Sequence data and also the results of clinical and parasitological examinations suggest that the snakes were definitive hosts forSarcocystisspp. that circulate in wild IH. Thus, it seems unlikely that the infected snakes had been legally bred. Our research shows that information on the infection of snakes withSarcocystisspp. may be used to assess compliance with regulations on the trade with wildlife species.

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Survey of bacteria associated with western corn rootworm life stages reveals no difference between insects reared in different soils

10.1101/365296 ◽

2018 ◽

Author(s):

Dalton C. Ludwick ◽

Aaron C. Ericsson ◽

Lisa N. Meihls ◽

Michelle L.J. Gregory ◽

Deborah L. Finke ◽

...

Keyword(s):

Pest Management ◽

Life Stage ◽

Diabrotica Virgifera Virgifera ◽

Western Corn Rootworm ◽

16S Rrna Genes ◽

Rrna Genes ◽

Corn Rootworm ◽

Life Stages ◽

Wide Range ◽

Different Soils

AbstractWestern corn rootworm (Diabrotica virgifera virgifera LeConte) is a serious pest of maize (Zea mays L.) in North America and parts of Europe. With most of its life cycle spent in the soil feeding on maize root tissues, this insect is likely to encounter and interact with a wide range of soil and rhizosphere microbes. Our knowledge of the role of microbes in pest management and plant health remains incomplete. An important component of an effective pest management strategy is to know which microorganisms are present that could play a role in life history or management. For this study, insects were reared in soils from different locations. Insects were sampled at each life stage to determine the possible core bacteriome. Additionally, soil was sampled at each life stage and resulting bacteria were identified to determine the contribution of soil to the rootworm bacteriome, if any. We analyzed the V4 hypervariable region of bacterial 16S rRNA genes with Illumina MiSeq to survey the different species of bacteria associated with the insects and the soils. The bacterial community associated with insects was significantly different from that in the soil. Some differences appear to exist between insects from non-diapausing and diapausing colonies while no significant differences in community composition existed between the insects reared on different soils. Despite differences in the bacteria present in immature stages and in male and female adults, there is a possible core bacteriome of approximately 16 operational taxonomic units (i.e., present across all life stages). This research may give insights into how resistance to Bt develops, improved nutrition in artificial rearing systems, and new management strategies.

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PHYLOGENETIC RELATIONSHIPS OF LEPTOBRACHIUM HASSELTII TSCHUDI, 1838 (AMPHIBIA, ANURA, MEGOPHRYIDAE) - DETECTION OF A POSSIBLE CRYPTIC SPECIES

TREUBIA ◽

10.14203/treubia.v44i0.3286 ◽

2018 ◽

Vol 44 ◽

pp. 15 ◽

Cited By ~ 1

Author(s):

Amir Hamidy ◽

Masafumi Matsui

Keyword(s):

Sequence Data ◽

Taxonomic Status ◽

Species Level ◽

16S Rrna Genes ◽

Rrna Genes ◽

12S Rrna ◽

The West ◽

Major Clade ◽

Dna Phylogeny ◽

Acoustic Data

By examining mitochondrial DNA phylogeny using 2424bp of sequence data 12S rRNA, tRNAval, and 16S rRNA genes, we evaluated the taxonomic relationships among Javan litter frogs Leptobrachium hasseltii from southern Sumatra, Java, and Bali. Leptobrachium hasseltii formed a well-supported monophyletic group, which comprised two major clades. One major clade represented the southern Sumatran and Javan populations and the other consisted of the population from Bali. The Javan and southern Sumatran clade included two subclades: the West Javan-southern Sumatran group and the Central Javan group. The genetic divergence between the two major clades (Bali vs. Java-Sumatra) suggested their separation happen at species level. Further studies using morphological and acoustic data are needed to determine the taxonomic status of Bali population.

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Cold-Active Shewanella glacialimarina TZS-4T nov. Features a Temperature-Dependent Fatty Acid Profile and Putative Sialic Acid Metabolism

Frontiers in Microbiology ◽

10.3389/fmicb.2021.737641 ◽

2021 ◽

Vol 12 ◽

Author(s):

Muhammad Suleman Qasim ◽

Mirka Lampi ◽

Minna-Maria K. Heinonen ◽

Berta Garrido-Zabala ◽

Dennis H. Bamford ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Sialic Acid ◽

Sea Ice ◽

Acid Metabolism ◽

Elevated Temperatures ◽

Consensus Sequence ◽

16S Rrna Genes ◽

Rrna Genes ◽

Wide Range ◽

Cold Active

Species of genus Shewanella are among the most frequently identified psychrotrophic bacteria. Here, we have studied the cellular properties, growth dynamics, and stress conditions of cold-active Shewanella strain #4, which was previously isolated from Baltic Sea ice. The cells are rod-shaped of ~2μm in length and 0.5μm in diameter, and they grow between 0 and 25°C, with an optimum at 15°C. The bacterium grows at a wide range of conditions, including 0.5–5.5% w/v NaCl (optimum 0.5–2% w/v NaCl), pH 5.5–10 (optimum pH 7.0), and up to 1mM hydrogen peroxide. In keeping with its adaptation to cold habitats, some polyunsaturated fatty acids, such as stearidonic acid (18:4n-3), eicosatetraenoic acid (20:4n-3), and eicosapentaenoic acid (20:5n-3), are produced at a higher level at low temperature. The genome is 4,456kb in size and has a GC content of 41.12%. Uniquely, strain #4 possesses genes for sialic acid metabolism and utilizes N-acetyl neuraminic acid as a carbon source. Interestingly, it also encodes for cytochrome c3 genes, which are known to facilitate environmental adaptation, including elevated temperatures and exposure to UV radiation. Phylogenetic analysis based on a consensus sequence of the seven 16S rRNA genes indicated that strain #4 belongs to genus Shewanella, closely associated with Shewanella aestuarii with a ~97% similarity, but with a low DNA–DNA hybridization (DDH) level of ~21%. However, average nucleotide identity (ANI) analysis defines strain #4 as a separate Shewanella species (ANI score=76). Further phylogenetic analysis based on the 92 most conserved genes places Shewanella strain #4 into a distinct phylogenetic clade with other cold-active marine Shewanella species. Considering the phylogenetic, phenotypic, and molecular characterization, we conclude that Shewanella strain #4 is a novel species and name it Shewanella glacialimarina sp. nov. TZS-4T, where glacialimarina means sea ice. Consequently, S. glacialimarina TZS-4T constitutes a promising model for studying transcriptional and translational regulation of cold-active metabolism.

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A Comparative Study: Taxonomic Grouping of Alkaline Protease Producing Bacilli

Polish Journal of Microbiology ◽

10.5604/17331331.1234992 ◽

2017 ◽

Vol 66 (1) ◽

pp. 39-56

Author(s):

Nilgun Tekin ◽

Arzu Coleri Cihan ◽

Basar Karaca ◽

Cumhur Cokmus

Keyword(s):

16S Rrna ◽

Alkaline Protease ◽

Phylogenetic Analyses ◽

Molecular Techniques ◽

16S Rrna Genes ◽

Rrna Genes ◽

Protease Production ◽

Rrna Gene ◽

Wide Range ◽

Its Pcr

Alkaline proteases have biotechnological importance due to their activity and stability at alkaline pH. 56 bacteria, capable of growing under alkaline conditions were isolated and their alkaline protease activities were carried out at different parameters to determine their optimum alkaline protease production conditions. Seven isolates were showed higher alkaline protease production capacity than the reference strains. The highest alkaline protease producing isolates (103125 U/g), E114 and C265, were identified as Bacillus licheniformis with 99.4% and Bacillus mojavensis 99.8% based on 16S rRNA gene sequence similarities, respectively. Interestingly, the isolates identified as Bacillus safensis were also found to be high alkaline protease producing strains. Genotypic characterizations of the isolates were also determined by using a wide range of molecular techniques (ARDRA, ITS-PCR, (GTG)5-PCR, BOX-PCR). These different techniques allowed us to differentiate the alkaliphilic isolates and the results were in concurrence with phylogenetic analyses of the 16S rRNA genes. While ITS-PCR provided the highest correlation with 16S rRNA groups, (GTG)5-PCR showed the highest differentiation at species and intra-species level. In this study, each of the biotechnologically valuable alkaline protease producing isolates was grouped into their taxonomic positions with multi-genotypic analyses.

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Computer-simulated RFLP analysis of 16S rRNA genes: identification of ten new phytoplasma groups

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.65000-0 ◽

2007 ◽

Vol 57 (8) ◽

pp. 1855-1867 ◽

Cited By ~ 233

Author(s):

Wei Wei ◽

Robert E. Davis ◽

Ing-Ming Lee ◽

Yan Zhao

Keyword(s):

16S Rrna ◽

Classification Scheme ◽

Rflp Analysis ◽

Plant Diseases ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Similarity Coefficients ◽

Wide Range

Phytoplasmas are cell wall-less bacteria that cause numerous plant diseases. As no phytoplasma has been cultured in cell-free medium, phytoplasmas cannot be differentiated and classified by the traditional methods which are applied to culturable prokaryotes. Over the past decade, the establishment of a phytoplasma classification scheme based on 16S rRNA restriction fragment length polymorphism (RFLP) patterns has enabled the accurate and reliable identification and classification of a wide range of phytoplasmas. In the present study, we expanded this classification scheme through the use of computer-simulated RFLP analysis, achieving rapid differentiation and classification of phytoplasmas. Over 800 publicly available phytoplasma 16S rRNA gene sequences were aligned using the clustal_x program and the aligned 1.25 kb fragments were exported to pDRAW32 software for in silico restriction digestion and virtual gel plotting. Based on distinctive virtual RFLP patterns and calculated similarity coefficients, phytoplasma strains were classified into 28 groups. The results included the classification of hundreds of previously unclassified phytoplasmas and the delineation of 10 new phytoplasma groups representing three recently described and seven novel putative ‘Candidatus Phytoplasma’ taxa.

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Group B Streptococcus colonization induces Prevotella and Megasphaera abundance-featured vaginal microbiome compositional change in non-pregnant women

PeerJ ◽

10.7717/peerj.7474 ◽

2019 ◽

Vol 7 ◽

pp. e7474 ◽

Cited By ~ 1

Author(s):

Xiaofeng Mu ◽

Changying Zhao ◽

Junjie Yang ◽

Xiaofang Wei ◽

Jiaming Zhang ◽

...

Keyword(s):

Pregnant Women ◽

Chinese Women ◽

Group B Streptococcus ◽

16S Rrna Genes ◽

Rrna Genes ◽

Vaginal Microbiome ◽

Positive Group ◽

Microbiome Diversity ◽

Chinese Cohort ◽

Group B

Background Previous studies have indicated that variations in the vaginal microbiome result in symptomatic conditions. Group B Streptococcus (GBS) is a significant neonatal pathogen and maternal vaginal colonization has been recognized as an important risk factor for neonatal disease. Therefore, it is important to discover the relationship between the composition of the vaginal microbiome and GBS colonization. This study explores the potential relationship between the composition of the vaginal microbiome and GBS colonization in non-pregnant Chinese women. Methods A total of 22 GBS-positive, non-pregnant women and 44 matched GBS-negative women were recruited for the current study. The composition of the vaginal microbiome was profiled by sequencing the 16S rRNA genes. The microbiome diversity and variation were then evaluated. Results The vaginal microbiome of the 66 subjects enrolled in the current study were compared and the results showed that GBS-positive women exhibited significant vaginal microbial differences compared with the GBS-negative women based on the analysis of similarities (r = 0.306, p < 0.01). The relative abundance of the bacterial genus Lactobacillus (p < 0.01) was significantly lower in the GBS-positive group, while the abundances of the bacterial genera Prevotella (p < 0.01), Megasphaera (p < 0.01), and Streptococcus (p < 0.01) were significantly higher in the GBS-positive group. Discussion The current study addressed significant variations across the communities of the vaginal microbiome in GBS-positive and GBS-negative women in a Chinese cohort, which paves the way for a larger cohort-based clinical validation study and the development of therapeutic probiotics in the future.

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Dix-seq: An integrated pipeline for fast amplicon data analysis

10.1101/2020.05.11.089748 ◽

2020 ◽

Author(s):

Yongjun wei ◽

Tianqi Ren ◽

Lei Zhang

Keyword(s):

Sequence Data ◽

Gene Diversity ◽

16S Rrna Genes ◽

Rrna Genes ◽

Sequencing Technologies ◽

Functional Gene Diversity ◽

Internal Transcribed Spacer Sequences ◽

The Common ◽

18S Rrna Genes ◽

Multiple Samples

AbstractThe amplicon derived from 16S rRNA genes, 18S rRNA genes, internal transcribed spacer sequences or other functional genes can be used to infer and evaluate microbial diversity or functional gene diversity. With the development of sequencing technologies, large amounts of amplicon data were generated. Several different software or pipelines had been developed for amplicon data analyses. However, most current software/pipelines require multistep and advanced programming skills. Moreover, they are often complex and time-consuming. Here, we introduced an integrated pipeline named Dix-seq for high-throughput amplicon sequence data processing (https://github.com/jameslz/dix-seq). Dix-seq integrates several different amplicon analysis algorithms and software for diversity analyses of multiple samples. Dix-seq analyzes amplicon sequences efficiently, and exports abundant visual results automatically with only one command in Linux environment. In summary, Dix-seq enables the common/advanced users to generate amplicon analysis results easily and offers a versatile and convenient tool for researchers.

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Effects of Gasterophilus pecorum infestation on the intestinal microbiota of the rewilded Przewalski’s horses in China

PLoS ONE ◽

10.1371/journal.pone.0251512 ◽

2021 ◽

Vol 16 (5) ◽

pp. e0251512

Author(s):

Dini Hu ◽

Yuzhu Chao ◽

Boru Zhang ◽

Chen Wang ◽

Yingjie Qi ◽

...

Keyword(s):

Intestinal Microbiota ◽

High Throughput Sequencing ◽

Nature Reserve ◽

Sequence Data ◽

Parasitic Infection ◽

16S Rrna Genes ◽

Rrna Genes ◽

Bioinformatics Analyses ◽

Gasterophilus Pecorum ◽

First Time

Horse botflies have been a threat to the Przewalski’s horses in the Kalamaili Nature Reserve in Xinjiang of China since their reintroduction to the original range. As larvae of these parasites could infest the intestine of a horse for months, they could interact with and alter the structure and composition of its intestinal microbiota, affecting adversely its health. Nonetheless, there are no such studies on the rewilded Przewalski’s horses yet. For the first time, this study characterizes the composition of the intestinal microbiota of 7 rewilded Przewalski’s horses infected severely by Gasterophilus pecorum following and prior to their anthelmintic treatment. Bioinformatics analyses of the sequence data obtained by amplicon high throughput sequencing of bacterial 16S rRNA genes showed that G. pecorum infestation significantly increased the richness of the intestinal microbial community but not its diversity. Firmicutes and Bacteroidetes were found the dominant phyla as in other animals, and the parasitic infestation decreased the F/B ratio largely by over 50%. Large reduction in relative abundances of the two genera Streptococcus and Lactobacillus observed with G. pecorum infestation suggested possible changes in colic and digestion related conditions of the infected horses. Variations on the relative abundance of the genus groups known to be pathogenic or symbiotic showed that adverse impact of the G. pecorum infestation could be associated with reduction of the symbiotic genera Lactobacillus and Bifidobacterium that are probiotics and able to promote immunity against parasitic infection.

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