scholarly journals PhaMers identifies novel bacteriophage sequences from thermophilic hot springs

2017 ◽  
Author(s):  
Jonathan Deaton ◽  
Feiqiao Brian Yu ◽  
Stephen R. Quake
Keyword(s):  
Hot Springs ◽  
Hot Spring ◽  
Sequence Similarity ◽  
Metagenomic Data ◽  
Metagenomic Sequencing ◽  
The Novel ◽  
Online Databases ◽  
Genome Prediction ◽  
Fungal Genomes

AbstractMetagenomic sequencing approaches have become popular for the purpose of dissecting environmental microbial diversity, leading to the characterization of novel microbial lineages. In addition of bacterial and fungal genomes, metagenomic analysis can also reveal genomes of viruses that infect microbial cells. Because of their small genome size and limited knowledge of phage diversity, discovering novel phage sequences from metagenomic data is often challenging. Here we describe PhaMers (Phagek-Mers). a phage identification tool that uses supervised learning to classify metagenomic contigs as phage or non-phage on the basis of tetranucleotide frequencies. a technique that does not depend on existing gene annotations. PhaMers compares the tetranucleotide frequencies of metagenomic contigs to phage and bacteria references from online databases. resulting in assignments of lower level phage taxonomy based on sequence similarity. Using PhaMers. we identified 103 novel phage sequences from hot spring samples of Yellowstone National Park based on data generated from a microfluidic-based minimetagenomic approach. We analyzed assembled contigs over 5 kbp in length using PhaMers and compared the results with those generated by VirSorter, a publicly available phage identification and annotation package. We analyzed the performance of phage genome prediction and taxonomic classification using PhaMers. and presented putative hosts and taxa for some of the novel phage sequences. Finally. mini-metagenomic occurrence profiles of phage and prokaryotic genomes were used to verify putative hosts.

scholarly journals Geochemical and metagenomic characterization of Jinata Onsen, a Proterozoic-analog hot spring, reveals novel microbial diversity including iron-tolerant phototrophs and thermophilic lithotrophs

2018 ◽  
Author(s):  
Lewis M. Ward ◽  
Airi Idei ◽  
Mayuko Nakagawa ◽  
Yuichiro Ueno ◽  
Woodward W. Fischer ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Ferrous Iron ◽  
Hot Springs ◽  
Hot Spring ◽  
Spatial Scales ◽  
Oxygenic Photosynthesis ◽  
Metagenomic Sequencing ◽  
Geochemical Conditions

AbstractHydrothermal systems, including terrestrial hot springs, contain diverse geochemical conditions that vary over short spatial scales due to progressive interaction between the reducing hydrothermal fluids, the oxygenated atmosphere, and in some cases seawater. At Jinata Onsen, on Shikinejima Island, Japan, an intertidal, anoxic, iron-rich hot spring mixes with the oxygenated atmosphere and seawater over short spatial scales, creating a diversity of chemical potentials and redox pairs over a distance ~10 m. We characterized the geochemical conditions along the outflow of Jinata Onsen as well as the microbial communities present in biofilms, mats, and mineral crusts along its traverse via 16S rDNA amplicon and genome-resolved shotgun metagenomic sequencing. The microbial community changed significantly downstream as temperatures and dissolved iron concentrations decreased and dissolved oxygen increased. Near the spring source, biomass is limited relative to downstream, and primary productivity may be fueled by oxidation of ferrous iron and molecular hydrogen by members of the Zetaproteobacteria and Aquificae. Downstream, the microbial community is dominated by oxygenic Cyanobacteria. Cyanobacteria are abundant and active even at ferrous iron concentrations of ~150 μM, which challenges the idea that iron toxicity limited cyanobacterial expansion in Precambrian oceans. Several novel lineages of Bacteria are also present at Jinata Onsen, including previously uncharacterized members of the Chloroflexi and Caldithrichaeota phyla, positioning Jinata Onsen as a valuable site for future characterization of these clades.ImportanceHigh temperatures and reducing conditions allow hot springs to support microbial communities that are very different from those found elsewhere on the surface of the Earth today; in some ways, these environments and the communities they support can be similar to environments that existed on the early Earth and that may exist on other planets. Here, we describe a novel hot spring system where hot, iron-rich but oxygen-poor water flows into the ocean, supporting a range of unique microbial communities. Metagenomic sequencing recovered many novel microbial lineages, including deep-branching and uniquely thermotolerant members of known groups. Comparison of the biological communities in the upstream part of the hot spring, potentially supported by biological iron and hydrogen oxidizing metabolisms, to downstream microbial mats, supported by oxygenic photosynthesis, provides insight into the potential productivity of life during Proterozoic time and on other planets where oxygenic photosynthesis is not possible.

Rhodocaloribacter litoris gen. nov., sp. nov., isolated from an intertidal hot spring

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Snædís H. Björnsdóttir ◽  
Sólveig K. Pétursdóttir ◽  
Elísabet E. Gudmundsdóttir ◽  
Edda Olgudóttir ◽  
Sigmar K. Stefansson ◽  
...  
Keyword(s):  
Hot Springs ◽  
Hot Spring ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Branched Chains

Red-pigmented strains of non-sporeforming, aerobic, chemoorganotrophic bacteria were isolated from intertidal hot springs in Laugarvík, NW-Iceland. Cells stained Gram-negative and formed pleomorphic rods that often had swollen ends and occurred singly or in filaments. Growth was observed at 40-65 °C (optimum at 60 °C), pH 6-9 (optimum at 6.5–8) and 0.5–5% (optimum at 1–2%) (w/v) NaCl. Strain ISCAR-4553T contained MK-7 as the main respiratory quinone and saturated iso and anteiso branched chains of 17 and 15 carbons as the main cellular fatty acids (83.4%). The G+C content of the DNA is 67.3 mol%. The highest 16S rRNA gene sequence similarity was with the genus Roseithermus (92.0%) and followed by Rhodothermus , Rubrivirga and Rubricoccus (88–90%). Genome and phenotype comparisons supported the affiliation of the novel isolates and the genus Roseithermus to the family Rhodothermaceae of the phylum Rhodothermaeota . The described isolates are proposed to be classified as representatives of a novel species belonging to a novel genus, with the name Rhodocaloribacter litoris gen. nov., sp. nov. The type strain is ISCAR-4553T (=DSM 110790T = ATCC TSD-179T).

scholarly journals Geobacillus lituanicus sp. nov.

2004 ◽  
Vol 54 (6) ◽  
pp. 1991-1995 ◽  
Author(s):  
Nomeda Kuisiene ◽  
Juozas Raugalas ◽  
Donaldas Chitavichius
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Gene Sequence Analysis ◽  
Pcr Rflp ◽  
Group 5

Obligately thermophilic, aerobic, proteolytic, endospore-forming strain N-3T was isolated from a high-temperature oilfield in Lithuania. 16S rRNA gene sequence analysis placed this strain in genetic group 5 of the endospore formers. Geobacillus thermoleovorans appeared to be the closest phylogenetic neighbour (99·4 % sequence similarity). The G+C content of strain N-3T was 52·5 mol% and matched the range established for the genus Geobacillus. Studies of DNA–DNA relatedness and morphological and physiological analyses enabled strain N-3T to be described as a member of the genus Geobacillus, but could not assign this strain to any other known species of this genus. Results of this polyphasic study allowed characterization of strain N-3T as a novel species in the genus Geobacillus – Geobacillus lituanicus sp. nov. This species can be distinguished from G. thermoleovorans and Geobacillus stearothermophilus on the basis of 16S rRNA gene PCR-RFLP assays with the restriction endonucleases AluI, HaeIII and TaqI. The type strain of the novel species is N-3T (=DSM 15325T=VKM B-2294T).

Magnetotactic bacteria in Tengchong hot springs, China

2020 ◽  
Author(s):  
Jia Liu ◽  
Wensi Zhang ◽  
Fang Yuan ◽  
Yongxin Pan ◽  
Wei Lin
Keyword(s):  
Hot Springs ◽  
Hot Spring ◽  
Extreme Environments ◽  
Magnetotactic Bacteria ◽  
Origin And Evolution ◽  
Water Columns ◽  
Genomic Analyses ◽  
Ph Range ◽  
Identification And Characterization

<p>Magnetotactic bacteria (MTB) biomineralize intracellular magnetic nanocrystals and can use the geomagnetic field to navigate towards specific microenvironments in water columns and sediments. MTB are a model system to study the mechanisms of microbial magnetoreception and biomineralization. The majority of MTB identified so far are from environments with pH values near neutral and at the normal range of temperature. MTB from extreme environments, such as hot springs, has not been observed and described until recently. However, our knowledge on extremophilic MTB is still very limited. Here we report the identification and characterization of various MTB in Tengchong hot springs, China, with a temperature range of 41.3-69.5 °C and a pH range of 7.1-8.6. Although MTB are diverse in cell morphology, they all form bullet-shaped magnetite magnetosomes organized into either one chain or multiple bundles of chains. Through genome-resolved metagenomics, we have reconstructed five genome bins of hot spring MTB that are all affiliated within the <em>Nitrspirae</em> phylum. Genomic analyses and metabolic reconstructions are now in progress. These results will help to better understand the extremophilic MTB and may shed new lights on the origin and evolution of microbial magnetoreception and biomineralization.</p>

Molecular characterization of hot spring cyanobacteria and evaluation of their photoprotective compounds

2012 ◽  
Vol 58 (6) ◽  
pp. 719-727 ◽  
Author(s):  
Rajesh P. Rastogi ◽  
Sunita Kumari ◽  
Richa ◽  
Taejun Han ◽  
Rajeshwar P. Sinha
Keyword(s):  
Amino Acids ◽  
High Performance ◽  
Hot Springs ◽  
Hot Spring ◽  
Polar Compounds ◽  
Rrna Gene ◽  
Negative Impacts ◽  
Highly Polar Compounds ◽  
The 16S Rrna Gene

Phylogenetic analysis of 4 cyanobacterial strains isolated from hot springs in Rajgir, India, was carried out using the 16S rRNA gene (1400 bp). These strains were identified as members of Chroococcales ( Cyanothece sp. strain HKAR-1) and Nostocales ( Nostoc sp. strain HKAR-2, Scytonema sp. strain HKAR-3, and Rivularia sp. strain HKAR-4). Furthermore, we evaluated the presence of ultraviolet-screening and (or) photoprotective compounds, such as mycosporine-like amino acids (MAAs) and scytonemin, in these cyanobacteria by using high-performance liquid chromatography. Well-characterized MAAs, including the critical and highly polar compounds shinorine, porphyra-334, and mycosporine-glycine, as well as several unknown MAAs, were found in these hot-spring-inhabiting microorganisms. The presence of scytonemin was detected only in Scytonema sp. strain HKAR-3 and Rivularia sp. strain HKAR-4. The results indicate that hot spring cyanobacteria, namely Cyanothece, Nostoc, Scytonema, and Rivularia, belonging to different groups possess various photoprotective compounds to cope up with the negative impacts of damaging radiations.

scholarly journals BiomeSeq: A Tool for the Characterization of Animal Microbiomes from Metagenomic Data

2021 ◽  
Author(s):  
Kelly A. Mulholland ◽  
Calvin L. Keeler
Keyword(s):  
Relative Abundance ◽  
Performance Metrics ◽  
Complete Characterization ◽  
Metagenomic Data ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Microbial Composition ◽  
Additional Species ◽  
User Friendly

Abstract BackgroundThe complete characterization of a microbiome is critical in elucidating the complex ecology of the microbial composition within healthy and diseased animals. Many microbiome studies characterize only the bacterial component, for which there are several well-developed sequencing methods, bioinformatics tools and databases available. The lack of comprehensive bioinformatics workflows and databases have limited efforts to characterize the other components existing in a microbiome. BiomeSeq is a tool for the analysis of the complete animal microbiome using metagenomic sequencing data. With its comprehensive workflow and customizable parameters and microbial databases, BiomeSeq can rapidly quantify the viral, fungal, bacteriophage and bacterial components of a sample and produce informative tables for analysis. ResultsSimulated datasets were constructed, which contained known abundances of microbial sequences, and several performance metrics were analyzed, including correlation of predicted abundance with known abundance, root mean square error and rate of speed. BiomeSeq demonstrated high precision (average of 99.52%) and sensitivity (average of 93.01%). BiomeSeq was employed in detecting and quantifying the respiratory microbiome of a commercial poultry broiler flock throughout its grow-out cycle from hatching to processing and successfully processed 780 million reads. For each microbial species detected, BiomeSeq calculated the normalized abundance, percent relative abundance, and coverage as well as the diversity for each sample. Rate of speed for each step in the pipeline, precision and accuracy were calculated to examine BiomeSeq’s performance using in silico sequencing datasets. When compared to bacterial results generated by the commonly used 16S rRNA sequencing method, BiomeSeq detected the same most abundant bacteria, including Gallibacterium, Corynebacterium and Staphylococcus, as well as several additional species. ConclusionsBiomeSeq provides for the detection and quantification of the microbiome from next-generation metagenomic sequencing data. This tool is implemented into a user-friendly container that requires one command and generates a table containing taxonomical information for each microbe detected. It also determines normalized abundance, percent relative abundance, genome coverage and sample diversity calculations for each sample.

scholarly journals Mycobacterium angelicum sp. nov., a non-chromogenic, slow-growing species isolated from fish and related to Mycobacterium szulgai

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4724-4729 ◽  
Author(s):  
Fazel Pourahmad ◽  
Mateja Pate ◽  
Matjaž Ocepek ◽  
Emanuele Borroni ◽  
Andrea M. Cabibbe ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
The Status ◽  
Polyphasic Characterization

The name ‘Mycobacterium angelicum’ dates back to 2003 when it was suggested for a slowly growing mycobacterium isolated from freshwater angelfish. This name is revived here and the novel species is proposed on the basis of the polyphasic characterization of four strains including the original one. The four strains presented 100 % 16S rRNA gene sequence similarity with Mycobacterium szulgai but clearly differed from M. szulgai for the milky white aspect of the colonies. The sequence similarity with the type strain of M. szulgai ranged, in eight additionally investigated genetic targets, from 78.9 to 94.3 %, an evident contrast with the close relatedness that emerged at the level of 16S rRNA gene. The average nucleotide identity between the genomes of M. szulgai DSM 44166T and strain 126/5/03T (type strain of the novel species) was 92.92 %, and supported the status of independent species. The confirmation of the name Mycobacterium angelicum sp. nov. is proposed, with strain 126/5/03T ( = CIP 109313T = DSM 45057T) as the type strain.

scholarly journals Comprehensive discovery of CRISPR-targeted terminally redundant sequences in the human gut metagenome: Viruses, plasmids, and more

2021 ◽  
Vol 17 (10) ◽  
pp. e1009428
Author(s):  
Ryota Sugimoto ◽  
Luca Nishimura ◽  
Phuong Thanh Nguyen ◽  
Jumpei Ito ◽  
Nicholas F. Parrish ◽  
...  
Keyword(s):  
De Novo ◽  
Sequence Similarity ◽  
Metagenomic Data ◽  
Marker Genes ◽  
Biological Entity ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Human Gut ◽  
Protein Coding ◽  
Viral Sequences

Viruses are the most numerous biological entity, existing in all environments and infecting all cellular organisms. Compared with cellular life, the evolution and origin of viruses are poorly understood; viruses are enormously diverse, and most lack sequence similarity to cellular genes. To uncover viral sequences without relying on either reference viral sequences from databases or marker genes that characterize specific viral taxa, we developed an analysis pipeline for virus inference based on clustered regularly interspaced short palindromic repeats (CRISPR). CRISPR is a prokaryotic nucleic acid restriction system that stores the memory of previous exposure. Our protocol can infer CRISPR-targeted sequences, including viruses, plasmids, and previously uncharacterized elements, and predict their hosts using unassembled short-read metagenomic sequencing data. By analyzing human gut metagenomic data, we extracted 11,391 terminally redundant CRISPR-targeted sequences, which are likely complete circular genomes. The sequences included 2,154 tailed-phage genomes, together with 257 complete crAssphage genomes, 11 genomes larger than 200 kilobases, 766 genomes of Microviridae species, 56 genomes of Inoviridae species, and 95 previously uncharacterized circular small genomes that have no reliably predicted protein-coding gene. We predicted the host(s) of approximately 70% of the discovered genomes at the taxonomic level of phylum by linking protospacers to taxonomically assigned CRISPR direct repeats. These results demonstrate that our protocol is efficient for de novo inference of CRISPR-targeted sequences and their host prediction.

scholarly journals Fontibacter flavus gen. nov., sp. nov., a member of the family ‘Cyclobacteriaceae’, isolated from a hot spring

2010 ◽  
Vol 60 (9) ◽  
pp. 2066-2070 ◽  
Author(s):  
Peter Kämpfer ◽  
Chiu-Chung Young ◽  
Wen-Ming Chen ◽  
P. D. Rekha ◽  
Kerstin Fallschissel ◽  
...  
Keyword(s):  
Type Strain ◽  
Hot Spring ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Polar Lipid Profile ◽  
Bright Orange ◽  
The Family ◽  
Southern Taiwan ◽  
Type Strains

The taxonomic position of a bright orange-pigmented bacterial strain, designated CC-GZM-130T, isolated from a water sample of the Guan-zing-ling hot spring, southern Taiwan, was studied. The strain was able to grow on nutrient agar at 25–40 °C and in the presence of 1–3 % (w/v) NaCl. Comparative analyses of the 16S rRNA gene sequence showed that the isolate was grouped in the vicinity of the genus Aquiflexum with the highest sequence similarity of 92.1 % to the type strain of Aquiflexum balticum, followed by sequence similarities of 92.0, 91.6 and 91.5 % to the type strains of Algoriphagus ornithinivorans, Algoriphagus hitonicola and Belliella baltica, respectively. The polyamine pattern showed that the major compound was sym-homospermidine. The quinone system was menaquinone MK-7. The polar lipid profile was composed predominantly of phosphatidylethanolamine, three polar lipids and one aminolipid. Minor amounts of other lipids were also detectable. The main characteristics of the fatty acid profiles of strain CC-GZM-130T, B. baltica and Aquiflexum balticum were similar, with iso-C15 : 0, iso-C17 : 1 ω9c and iso-C17 : 0 3-OH as the major fatty acids, but some qualitative and quantitative differences were observed. The DNA G+C content of the novel strain was 53.2 mol%. The isolate clearly differed genotypically and phenotypically from representatives of the most closely related genera. On the basis of these differences, a novel species in a new genus, Fontibacter flavus gen. nov., sp. nov., is proposed with CC-GZM-130T (=CCUG 57694T=CCM 7650T) as the type strain of the type species.

scholarly journals The Effect of Spring Water Geochemistry on Copper Proteins in Tengchong Hot Springs, China

2020 ◽  
Vol 86 (13) ◽  
Author(s):  
Shreya Srivastava ◽  
Hailiang Dong ◽  
Brandon R. Briggs
Keyword(s):  
High Temperature ◽  
Binding Proteins ◽  
Hot Springs ◽  
Hot Spring ◽  
Metagenomic Data ◽  
Copper Proteins ◽  
Ph Gradients ◽  
Quinol Oxidase ◽  
Binding Domains ◽  
Wide Range

ABSTRACT Copper (Cu) is an essential trace metal cofactor for a variety of proteins; however, excess Cu is toxic to most organisms. Cu homeostasis is maintained by a complex machinery of Cu binding proteins that control the uptake, transport, sequestration, and efflux of Cu ions. Despite the importance of Cu binding proteins in electron transfer, substrate oxidation, superoxide dismutation, and denitrification, little information exists about microbial Cu utilization in extreme environments, where the geochemical conditions may affect Cu bioavailability. Using metagenomic data from 9 hot springs in Tengchong, China, which range in temperature from 42°C to 96°C and in pH from 2.3 to 9, the effects of pH, temperature, and spring geochemistry on the distribution of Cu binding domains of proteins and oxidoreductases were studied. Dissolved Cu and Cu binding domains were detected across all temperature and pH gradients. Cu binding domains of cytochrome c oxidase subunits, heavy-metal-associated domains, and nitrous oxide reductase were detected at all sites. DoxB, a quinol oxidase, and other quinol oxidase subunits were the dominant Cu binding oxidoreductase subunits present at low-pH and high-temperature sites, whereas cbb3-type cytochrome c oxidase subunits were dominant at high-pH and high-temperature sites. Additionally, aa3-type cytochrome c oxidase was more prominent than cbb3-type cytochrome c oxidase under circumneutral-pH conditions. This suggests that the type of cytochrome c oxidase pathway and the Cu proteins employed by microbes to carry out important functions such as energy acquisition and efflux of excess Cu are affected by the physicochemical conditions of the springs. IMPORTANCE Copper is present in a variety of proteins and is required to carry out essential functions by all organisms. However, in hot spring environments, copper availability may be limited due to the high temperatures and the wide range in pH. The significance of our research is in relating the physicochemical environment to the distribution of copper proteins across hot spring environments, which provides increased understanding of primary functions and adaptions in these environments.

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