scholarly journals Short Communication: The emergence and rise of indigenous thermophilic bacteria exploration from hot springs in Indonesia

2020 ◽  
Vol 21 (11) ◽  
Author(s):  
Kenny Lischer ◽  
ANANDA BAGUS RICHKY DIGDAYA PUTRA ◽  
Brian Wirawan Guslianto ◽  
Forbes Avila ◽  
Sarah Grace Sitorus ◽  
...  
Keyword(s):  
High Temperature ◽  
16S Rrna ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Short Communication ◽  
Hot Springs ◽  
Thermophilic Bacteria ◽  
Whole Genome ◽  
Thermostable Enzymes ◽  
The Pacific

Abstract. Lischer K, Putra ABRD, Guslianto BW, Avilla F, Sitorus SG, Nugraha Y, Sarmoko. 2020. Short Communication: The emergence and rise of indigenous thermophilic bacteria exploration from hot springs in Indonesia. Biodiversitas 21: 5474-5481. Indonesia is an archipelagic country located in the pacific ring of fire, and is estimated to cause numerous hot springs spread across the country. In addition, small living microbes have been explored in these locations since 1985. These microbes possess the ability to survive in areas with high temperature (more than 40oC-90oC), and are therefore termed thermophiles. Hence, massive explorations have been conducted on Java island and other unexplored areas at Sumatra to Papua in New Guinea islands. Moreover, a total of 71 hot springs characterized by the presence of thermophilic bacteria have been explored in Indonesia. These investigations ensue with various approaches, including through conventional and microbiological, 16S rRNA, as well as whole-genome sequencing methods. In addition to species exploration, the application of thermophiles has become a topic of interest from 1999, especially based on thermostable enzymes with the capacity to maintain activity at high-temperature conditions. These include amylase, protease, lipase, xylanase, esterase, and cellulase as the most common isolated form, which indicates the existence of significant extractable potentials. Hence, there is a need for further research in terms of both exploration and application purposes.

scholarly journals Short communication: Persistent contamination by Listeria monocytogenes of bovine raw milk investigated by whole-genome sequencing

2019 ◽  
Vol 102 (7) ◽  
pp. 6032-6036
Author(s):  
M. Ricchi ◽  
E. Scaltriti ◽  
G. Cammi ◽  
C. Garbarino ◽  
N. Arrigoni ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Short Communication ◽  
Raw Milk ◽  
Whole Genome

scholarly journals Whole-genome sequencing uncovers cryptic and hybrid species among Atlantic and Pacific cod-fish

2015 ◽  
Author(s):  
Katrín Halldórsdóttir ◽  
Einar Árnason
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Atlantic Cod ◽  
Walleye Pollock ◽  
Evolutionary Status ◽  
Whole Genome ◽  
Hybrid Speciation ◽  
Hybrid Species ◽  
The Pacific ◽  
Starting Point

Speciation often involves the splitting of a lineage and the adaptation of daughter lineages to different environments. It may also involve the merging of divergent lineages, thus creating a stable homoploid hybrid species1that constructs a new ecological niche by transgressing2the ecology of the parental types. Hybrid speciation may also contribute to enigmatic and cryptic biodiversity in the sea.3,4The enigmatic walleye pollock, which is not a pollock at all but an Atlantic cod that invaded the Pacific 3.8 Mya,5differs considerably from its presumed closest relatives, the Pacific and Atlantic cod. Among the Atlantic cod, shallow-water coastal and deep-water migratory frontal ecotypes are associated with highly divergent genomic islands;6,7however, intermediates remain an enigma.8Here, we performed whole-genome sequencing of over 200 individuals using up to 33 million SNPs based on genotype likelihoods9and showed that the evolutionary status of walleye pollock is a hybrid species: it is a hybrid between Arctic cod and Atlantic cod that transgresses the ecology of its parents. For the first time, we provide decisive evidence that the Atlantic cod coastal and frontal ecotypes are separate species that hybridized, leading to a true-breeding hybrid species that differs ecologically from its parents. We refute monophyly and dichotomous branching of these taxa, and stress the importance of looking beyond branching trees at admixture and hybridity. Our study demonstrates the power of whole-genome sequencing and population genomics in providing deep insights into fundamental processes of speciation. Our study was a starting point for further work aimed at examining the criteria of hybrid speciation,10selection, sterility and structural chromosomal variation11among cod-fish, which are among the most important fish stocks in the world. The hybrid nature of both the walleye pollock and Atlantic cod raises the question concerning the extent to which very profitable fisheries12,13depend on hybrid vigour. Our results have implications for management of marine resources in times of rapid climate change.14,15

scholarly journals Reliable Identification of Environmental Pseudomonas Isolates Using the rpoD Gene

2020 ◽  
Vol 8 (8) ◽  
pp. 1166
Author(s):  
Léa Girard ◽  
Cédric Lood ◽  
Hassan Rokni-Zadeh ◽  
Vera van Noort ◽  
Rob Lavigne ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Low Cost ◽  
Rrna Gene ◽  
Whole Genome ◽  
Comprehensive Overview ◽  
Rpod Gene ◽  
The 16S Rrna Gene

The taxonomic affiliation of Pseudomonas isolates is currently assessed by using the 16S rRNA gene, MultiLocus Sequence Analysis (MLSA), or whole genome sequencing. Therefore, microbiologists are facing an arduous choice, either using the universal marker, knowing that these affiliations could be inaccurate, or engaging in more laborious and costly approaches. The rpoD gene, like the 16S rRNA gene, is included in most MLSA procedures and has already been suggested for the rapid identification of certain groups of Pseudomonas. However, a comprehensive overview of the rpoD-based phylogenetic relationships within the Pseudomonas genus is lacking. In this study, we present the rpoD-based phylogeny of 217 type strains of Pseudomonas and defined a cutoff value of 98% nucleotide identity to differentiate strains at the species level. To validate this approach, we sequenced the rpoD of 145 environmental isolates and complemented this analysis with whole genome sequencing. The rpoD sequence allowed us to accurately assign Pseudomonas isolates to 20 known species and represents an excellent first diagnostic tool to identify new Pseudomonas species. Finally, rpoD amplicon sequencing appears as a reliable and low-cost alternative, particularly in the case of large environmental studies with hundreds or thousands of isolates.

scholarly journals Whole-Genome Sequencing of Lentibacillus sp. Strain JNUCC-1, Isolated from Fermented Anchovy Sauce (Myeolchi Aekjeot)

2020 ◽  
Vol 9 (15) ◽  
Author(s):  
Hoo-Dhon Byun ◽  
Chang-Gu Hyun
Keyword(s):  
16S Rrna ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Novel Species ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
Content Type ◽  
Anchovy Sauce

Lentibacillus sp. strain JNUCC-1 was isolated from Korean traditionally fermented anchovy sauce. The 16S rRNA sequence of JNUCC-1 showed 95.2% and 95.1% similarity to Lentibacillus populi WD4L-1T and Virgibacillus siamensis MS3-4T, respectively, indicating that it is a novel species. The whole-genome sequence, which contains 3,687,469 bp and 3,833 genes in 3 contigs, is reported.

scholarly journals Mining underutilized whole-genome sequencing projects to improve 16S rRNA databases

2021 ◽  
Author(s):  
Ben Nolan ◽  
Florence Abram ◽  
Fiona Brennan ◽  
Ashleigh Holmes ◽  
Vincent O’Flaherty ◽  
...  
Keyword(s):  
16S Rrna ◽  
Whole Genome Sequencing ◽  
16S Rdna ◽  
Genome Sequencing ◽  
Sequence Variants ◽  
Whole Genome ◽  
Short Reads ◽  
A Genome ◽  
Rrna Sequences ◽  
16S Rrna Sequences

AbstractCurrent approaches to interpreting 16S rDNA amplicon data are hampered by several factors. Among these are database inaccuracy or incompleteness, sequencing error, and biased DNA/RNA extraction. Existing 16S rRNA databases source the majority of sequences from deposited amplicon sequences, draft genomes, and complete genomes. Most of the draft genomes available are assembled from short reads. However, repeated ribosomal regions are notoriously difficult to assemble well from short reads, and as a consequence the short-read-assembled 16S rDNA region may be an amalgamation of different loci within the genome. This complicates high-resolution community analysis, as a draft genome’s 16S rDNA sequence may be a chimera of multiple loci; in such cases, the draft-derived sequences in a database may not represent a 16S rRNA sequence as it occurs in biology. We present Focus16, a pipeline for improving 16S rRNA databases by mining NCBI’s Sequence Read Archive for whole-genome sequencing runs that could be reassembled to yield additional 16S rRNA sequences. Using riboSeed (a genome assembly tool for correcting rDNA misassembly), Focus16 provides a way to augment 16S rRNA databases with high-quality re-assembled sequences. In this study, we augmented the widely-used SILVA 16S rRNA database with the novel sequences disclosed by Focus16 and re-processed amplicon sequences from several benchmarking datasets with DADA2. Using this augmented SILVA database increased the number of amplicon sequence variants that could be assigned taxonomic annotations. Further, fine-scale classification was improved by revealing ambiguities. We observed, for example, that amplicon sequence variants (ASVs) may be assigned to a specific genus where Focus16-correction would indicate that the ASV is represented in two or more genera. Thus, we demonstrate that improvements can be made to taxonomic classification by incorporating these carefully re-assembled 16S rRNA sequences, and we invite the community to expand our work to augment existing 16S rRNA reference databases such as SILVA, GreenGenes, and RDP.

scholarly journals Hemicellulosic biomass conversion by Moroccan hot spring Bacillus paralicheniformis CCMM B940 evidenced by glycoside hydrolase activities and whole genome sequencing

3 Biotech ◽  
2021 ◽  
Vol 11 (8) ◽  
Author(s):  
Soufiane Maski ◽  
Serigne Inssa Ngom ◽  
Bahia Rached ◽  
Taha Chouati ◽  
Mohamed Benabdelkhalek ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Plant Cell Wall ◽  
Hot Spring ◽  
Thermophilic Bacteria ◽  
Draft Genome ◽  
Glycoside Hydrolases ◽  
Whole Genome ◽  
A Genome ◽  
Bacillus Paralicheniformis

AbstractThermophilic bacteria, especially from the genus Bacillus, constitute a huge potential source of novel enzymes that could be relevant for biotechnological applications. In this work, we described the cellulose and hemicellulose-related enzymatic activities of the hot spring Bacillus aerius CCMM B940 from the Moroccan Coordinated Collections of Microorganisms (CCMM), and revealed its potential for hemicellulosic biomass utilization. Indeed, B940 was able to degrade complex polysaccharides such as xylan and lichenan and exhibited activity towards carboxymethylcellulose. The strain was also able to grow on agriculture waste such as orange and apple peels as the sole carbon source. Whole-genome sequencing allowed the reclassification of CCMM B940 previously known as B. aerius into Bacillus paralicheniformis since the former species name has been rejected. The draft genome reported here is composed of 38 contigs resulting in a genome of 4,315,004 bp and an average G + C content of 45.87%, and is an important resource for illuminating the molecular mechanisms of carbohydrate metabolism. The annotated genomic sequences evidenced more than 52 genes encoding glycoside hydrolases and pectate lyases belonging to 27 different families of CAZymes that are involved in the degradation of plant cell wall carbohydrates. Genomic predictions in addition to in vitro experiments have revealed broad hydrolytic capabilities of the strain, thus reinforcing its relevance for biotechnology applications.

scholarly journals Hymenobacter terrestris sp. nov. and Hymenobacter lapidiphilus sp. nov., isolated from regoliths in Antarctica

2020 ◽  
Vol 70 (12) ◽  
pp. 6364-6372
Author(s):  
Ivo Sedláček ◽  
Roman Pantůček ◽  
Michal Zeman ◽  
Pavla Holochová ◽  
Ondrej Šedo ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Type Strain ◽  
Whole Genome Sequencing Data ◽  
Rrna Gene ◽  
Whole Genome ◽  
Content Type ◽  
Link Type

A group of four psychrotrophic bacterial strains was isolated on James Ross Island (Antarctica) in 2013. All isolates, originating from different soil samples, were collected from the ice-free northern part of the island. They were rod-shaped, Gram-stain-negative, and produced moderately slimy red-pink pigmented colonies on R2A agar. A polyphasic taxonomic approach based on 16S rRNA gene sequencing, whole-genome sequencing, MALDI-TOF MS, rep-PCR analyses, chemotaxonomic methods and extensive biotyping was used to clarify the taxonomic position of these isolates. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolates belonged to the genus Hymenobacter . The closest relative was Hymenobacter humicola CCM 8763T, exhibiting 98.3 and 98.9% 16S rRNA pairwise similarity with the reference isolates P5342T and P5252T, respectively. Average nucleotide identity, digital DNA–DNA hybridization and core gene distances calculated from the whole-genome sequencing data confirmed that P5252T and P5342T represent two distinct Hymenobacter species. The menaquinone systems of both strains contained MK-7 as the major respiratory quinone. The predominant polar lipids for both strains were phosphatidylethanolamine and one unidentified glycolipid. The major components in the cellular fatty acid composition were summed feature 3 (C16:1 ω7c/C16:1ω6c), C16:1ω5c, summed feature 4 (anteiso-C17:1 B/iso-C17:1 I), anteiso-C15:0 and iso-C15 : 0 for all isolates. Based on the obtained results, two novel species are proposed, for which the names Hymenobacter terrestris sp. nov. (type strain P5252T=CCM 8765T=LMG 31495T) and Hymenobacter lapidiphilus sp. nov. (type strain P5342T=CCM 8764T=LMG 30613T) are suggested.

scholarly journals Emergence of Carbapenem-Resistant Pseudomonas asiatica Producing NDM-1 and VIM-2 Metallo-β-Lactamases in Myanmar

2019 ◽  
Vol 63 (8) ◽  
Author(s):  
Mari Tohya ◽  
Tatsuya Tada ◽  
Shin Watanabe ◽  
Kyoko Kuwahara-Arai ◽  
Khwar Nyo Zin ◽  
...  
Keyword(s):  
16S Rrna ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Gene Encoding ◽  
Medical Settings ◽  
Content Type ◽  
Carbapenem Resistant ◽  
Genes Encoding ◽  
16S Rrna Methylase

ABSTRACT Pseudomonas asiatica is a recently proposed species of the genus Pseudomonas. This study describes eight isolates of carbapenem-resistant P. asiatica harboring blaNDM-1 and blaVIM-2, genes encoding metallo-β-lactamase (MBL). These isolates were obtained from urine samples of patients hospitalized in Myanmar. These isolates were resistant to carbapenems but susceptible to colistin. All eight isolates were positive for a carbapenemase inactivation method, CIMTrisII, and seven were positive on an immunochromatographic assay for NDM-type MBL. One isolate was highly resistant to aminoglycosides. Whole-genome sequencing showed that seven isolates harbored blaNDM-1 and one harbored blaVIM-2, with these genes located on the chromosome. One isolate harbored blaNDM-1 and rmtC, a gene encoding 16S rRNA methylase. Five types of genomic environments surrounding blaNDM-1 and blaVIM-2 were detected in these eight isolates, with four isolates having the same type. These data indicate that P. asiatica isolates harboring genes encoding carbapenemases, including blaNDM-1 and blaVIM-2, are spreading in medical settings in Myanmar.

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