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 ◽  
...  

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.

2020 ◽  
Vol 21 (11) ◽  
Author(s):  
Kenny Lischer ◽  
ANANDA BAGUS RICHKY DIGDAYA PUTRA ◽  
Brian Wirawan Guslianto ◽  
Forbes Avila ◽  
Sarah Grace Sitorus ◽  
...  

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.


2018 ◽  
Vol 7 (18) ◽  
Author(s):  
Wai-Sing Chan ◽  
Chun-Hang Au ◽  
Henry Chi-Ming Leung ◽  
Dona N. Ho ◽  
Tsun-Leung Chan ◽  
...  

Isolation of Helicobacter cinaedi from a positive blood culture requires prolonged and stringent subculture conditions. Direct whole-genome sequencing (WGS) of a positive blood culture may provide timely treatment-associated genetic information.


2019 ◽  
Vol 8 (15) ◽  
Author(s):  
Moon Y. F. Tay ◽  
Frederick Adzitey ◽  
Stella Amelia Sultan ◽  
Joseph Makija Tati ◽  
Kelyn L. G. Seow ◽  
...  

Here, we report the draft genome sequences of 16 nontyphoidal Salmonella enterica isolates obtained from locally produced meats in Tamale, Ghana, which are commonly consumed by most natives as an important protein source. The draft genomes will help provide a molecular snapshot of Salmonella enterica isolates found in these retail meats in Tamale.


2020 ◽  
Vol 9 (21) ◽  
Author(s):  
Daniel L. Vera ◽  
Arman Seuylemezian ◽  
Kyle S. Landry ◽  
Ryan Hendrickson

ABSTRACT Whole-genome sequencing and annotation have allowed planetary protection engineers to assess the functional capabilities of microorganisms isolated from spacecraft hardware and associated surfaces. Here, we report draft genomes of six strains isolated from the InSight mission, determined using Oxford Nanopore- and Illumina-based sequencing.


2019 ◽  
Vol 8 (17) ◽  
Author(s):  
Kevin Cole ◽  
Dona Foster ◽  
Julie E. Russell ◽  
Tanya Golubchik ◽  
Martin Llewelyn ◽  
...  

Members of the genus Staphylococcus have been isolated from humans, animals, and the environment. Accurate identification with whole-genome sequencing requires access to data derived from type strains.


2019 ◽  
Vol 9 (10) ◽  
pp. 3213-3223 ◽  
Author(s):  
Giovanna Cáceres ◽  
María E. López ◽  
María I. Cádiz ◽  
Grazyella M. Yoshida ◽  
Ana Jedlicki ◽  
...  

Nile tilapia (Oreochromis niloticus) is one of the most cultivated and economically important species in world aquaculture. Intensive production promotes the use of monosex animals, due to an important dimorphism that favors male growth. Currently, the main mechanism to obtain all-male populations is the use of hormones in feeding during larval and fry phases. Identifying genomic regions associated with sex determination in Nile tilapia is a research topic of great interest. The objective of this study was to identify genomic variants associated with sex determination in three commercial populations of Nile tilapia. Whole-genome sequencing of 326 individuals was performed, and a total of 2.4 million high-quality bi-allelic single nucleotide polymorphisms (SNPs) were identified after quality control. A genome-wide association study (GWAS) was conducted to identify markers associated with the binary sex trait (males = 1; females = 0). A mixed logistic regression GWAS model was fitted and a genome-wide significant signal comprising 36 SNPs, spanning a genomic region of 536 kb in chromosome 23 was identified. Ten out of these 36 genetic variants intercept the anti-Müllerian (Amh) hormone gene. Other significant SNPs were located in the neighboring Amh gene region. This gene has been strongly associated with sex determination in several vertebrate species, playing an essential role in the differentiation of male and female reproductive tissue in early stages of development. This finding provides useful information to better understand the genetic mechanisms underlying sex determination in Nile tilapia.


2020 ◽  
Vol 110 (7) ◽  
pp. 1255-1259
Author(s):  
Emily Giroux ◽  
Guillaume J. Bilodeau

The filamentous ascomycete fungus Lachnellula willkommii is the causal agent of European larch canker (ELC), one of the most destructive diseases of larch in Europe and a regulated plant pathogen of quarantine significance in Canada and the United States. L. willkommii was first detected in Massachusetts, North America in 1927 on a larch plantation cultivated with nursery stock imported from Great Britain. Despite the decades of practices aimed at eliminating the pathogen, it has reappeared in coastal areas of Canada and the United States. There is concern ELC could spread throughout the range of eastern larch, a transcontinental species typical of the Boreal forest that spans the North American landscape. There is geographic range overlap between several nonpathogenic indigenous Lachnellula species and the reported distribution of L. willkommii in North America. Morphological and biological methods to distinguish L. willkommii are often inadequate as the fungus does not always produce the phenotypic structures that distinguish it from these other saprophytic Lachnellula species. Whole genome sequencing technologies were used to obtain the draft genome sequences of L. willkommii and six other Lachnellula species. Molecular markers identified from the genomic data may be used to discriminate L. willkommii from its nonpathogenic relatives.


2020 ◽  
Vol 9 (11) ◽  
Author(s):  
Anthony Mannion ◽  
Tina McCollester ◽  
Alexander Sheh ◽  
Zeli Shen ◽  
Hilda Holcombe ◽  
...  

A fast-growing Mycobacterium species was cultured from draining, purulent lesions on the caudal abdomen of a 12-year-old male domestic long-haired cat. Whole-genome sequencing identified the organism as Mycobacterium porcinum.


2020 ◽  
Author(s):  
Alexander Smetanin ◽  
Nikita Moshkov ◽  
Tatiana V. Tatarinova

AbstractSummaryWe developed PyLAE - a new tool for determining local ancestry along a genome using whole-genome sequencing data or high-density genotyping experiments. PyLAE can process an arbitrarily large number of ancestral populations (with or without an informative prior). Since PyLAE does not involve estimation of many parameters, it can process thousands of genomes within a day. Computational efficiency, straightforward presentation of results, and an ease of installation makes PyLAE a useful tool to study admixed populations.Availability and implementationThe source code and installation manual are available at https://github.com/smetam/pylae.


2021 ◽  
Author(s):  
Severin Einspanier ◽  
Tamara Susanto ◽  
Nicole Metz ◽  
Pieter J. Wolters ◽  
Vivianne G.A.A. Vleeshouwers ◽  
...  

Early blight of potato is caused by the fungal pathogen Alternaria solani and is an increasing problem worldwide. The primary strategy to control the disease is applying fungicides such as succinate dehydrogenase inhibitors (SDHI). SDHI-resistant strains, showing reduced sensitivity to treatments, appeared in Germany in 2013, five years after introduction of SDHIs. Two primary mutations in the Sdh complex (SdhB-H278Y and SdhC-H134R) have been frequently found throughout Europe. How these resistances arose and spread, and whether they are linked to other genomic features, remains unknown. We performed whole-genome sequencing for A. solani isolates from potato fields across Europe (Germany, Sweden, Belgium, and Serbia) to better understand the pathogen's genetic diversity in general and understand the development and spread of the genetic mutations that lead to SDHI resistance. We used ancestry analysis and phylogenetics to determine the genetic background of 48 isolates. The isolates can be grouped into 7 genotypes. These genotypes do not show a geographical pattern but appear spread throughout Europe. The Sdh mutations appear in different genetic backgrounds, suggesting they arose independently, and the observed admixtures might indicate a higher adaptive potential in the fungus than previously thought. Our research gives insights into the genetic diversity of A. solani on a genome level. The mixed occurrence of different genotypes and apparent admixture in the populations indicate higher genomic complexity than anticipated. The conclusion that SDHI tolerance arose multiple times independently has important implications for future fungicide resistance management strategies. These should not solely focus on preventing the spread of isolates between locations but also on limiting population size and the selective pressure posed by fungicides in a given field to avoid the rise of new mutations in other genetic backgrounds.


Sign in / Sign up

Export Citation Format

Share Document