scholarly journals Assessment and Characterization of Xylanolytic Bacteria Isolated from the Gut of Microtermes Obesi for Biomass Pretreatment

2021 ◽  
Author(s):  
Iram Batool ◽  
Falak Sher Khan ◽  
Muhammad Awais ◽  
Dawood Ahmed ◽  
Sami Ullah Khan ◽  
...  
Keyword(s):  
Corn Stover ◽  
Rice Straw ◽  
16S Rrna Gene Sequencing ◽  
Major Constituent ◽  
Rrna Gene ◽  
Bacterial Isolates ◽  
Cotton Stalk ◽  
Termite Gut ◽  
Chemical Pretreatments ◽  
Rrna Gene Sequencing

Abstract The aim of current research was to examine the potential for the production of hemicelluloses degrading enzymes from bacteria harbor in termite gut. The research was also focused on the conversion of lignocellulosic biomass (Corn stover, rice straw and cotton stalk) into fermentable sugars by using enzymes from the bacterial isolates. The bacterial isolates from termite gut were screened for their ability to degrade xylan that is the major constituent of hemicelluloses. Two bacterial isolates were chosen and identified by 16S rRNA gene sequencing. Both isolates TGB9 and TGB10 belong to Bacillus geneus. The isolates have shown higher xylan degrading activity at 50 oC and optimum pH was 6.0. Xylanases from isolate TGB9 and TGB10 were utilized for sccharification of agricultural substrates (stover, rice straw and cotton stalk). As a result higher contents of reducing sugars were observed from corn stover. Xylanases from isolate TGB9 produced higher yields of reducing sugar than isolate TGB10. A comparative study was also performed among chemical pretreatment and xylanases from bacterial isolates. For this purpose agricultural substrates were also treated with H2SO4 and NaOH. Xylanases produced by TGB9 and TGB10 released higher content of sugar from agricultural substrates than chemical pretreatments. So it is concluded that termite gut have bacteria that can hydrolyze hemicelluloses more efficiently than chemicals.

scholarly journals Profiling the microbial community of a Triassic halite deposit in Northern Ireland: an environment with significant potential for biodiscovery

2019 ◽  
Vol 366 (22) ◽  
Author(s):  
Julianne Megaw ◽  
Stephen A Kelly ◽  
Thomas P Thompson ◽  
Timofey Skvortsov ◽  
Brendan F Gilmore
Keyword(s):  
Northern Ireland ◽  
16S Rrna Gene Sequencing ◽  
Antimicrobial Activities ◽  
Chemical Diversity ◽  
Hypersaline Environment ◽  
Rrna Gene ◽  
Bacterial Isolates ◽  
Culture Independent ◽  
Rrna Gene Sequencing ◽  
County Antrim

ABSTRACT Kilroot salt mine, a Triassic halite deposit located in County Antrim, Northern Ireland, is the only permanent hypersaline environment on the island of Ireland. In this study, the microbiome of this unstudied environment was profiled for the first time using conventional and enhanced culturing techniques, and culture independent metagenomic approaches. Using both conventional isolation plates and iChip devices, 89 halophilic archaeal isolates from six known genera, and 55 halophilic or halotolerant bacterial isolates from 18 genera were obtained, based on 16S rRNA gene sequencing. The archaeal isolates were similar to those previously isolated from other ancient halite deposits, and as expected, numerous genera were identified in the metagenome which were not represented among the culturable isolates. Preliminary screening of a selection of isolates from this environment identified antimicrobial activities against a panel of clinically important bacterial pathogens from 15 of the bacterial isolates and one of the archaea. This, alongside previous studies reporting the discovery of novel biocatalysts from the Kilroot mine microbiome, suggests that this environment may be a new, untapped source of of chemical diversity with high biodiscovery potential.

Chitinolytic bacteria in the intestinal tract of Japanese coastal fishes

2006 ◽  
Vol 52 (12) ◽  
pp. 1158-1163 ◽  
Author(s):  
Shiro Itoi ◽  
Toshihiro Okamura ◽  
Yuki Koyama ◽  
Haruo Sugita
Keyword(s):  
16S Rrna ◽  
Intestinal Tract ◽  
Intestinal Bacteria ◽  
16S Rrna Gene Sequencing ◽  
Colloidal Chitin ◽  
Rrna Gene ◽  
Bacterial Isolates ◽  
Coastal Fish ◽  
Chitinolytic Bacteria ◽  
Rrna Gene Sequencing

Intestinal bacteria from several coastal fish species were screened on 1/20 PYBG medium containing 0.2% colloidal chitin, and 361 bacteria capable of decomposing colloidal chitin were isolated. These isolates were subsequently screened on media containing either 0.5% α-chitin or 0.5% β-chitin resulting in the identification of 31 α-chitinolytic and 275 β-chitinolytic bacterial isolates. Partial 16S rRNA gene sequencing was carried out and homology searches of the resultant sequences against the DDBJ, EMBL, and GenBank databases revealed that the majority (99%) of the chitinolytic bacteria isolated belonged to the Vibrionaceae. Phylogenetic analysis using a Bayesian approach showed that the α-chitinolytic bacteria belonging to the Vibrionaceae formed a separate cluster from the non-α-chitinolytic bacteria in the Vibrionaceae.Key words: chitinolytic bacteria, 16S rRNA, α-chitin, coastal fish, intestinal bacteria.

scholarly journals Integrative analysis of the gut microbiota and metabolome in rats treated with rice straw biochar by 16S rRNA gene sequencing and LC/MS-based metabolomics

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Jie Han ◽  
Jun Meng ◽  
Shuya Chen ◽  
Chuang Li
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Rice Straw ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Metabolic Phenotype ◽  
Rrna Gene ◽  
Tetradecanoic Acid ◽  
Rice Straw Biochar ◽  
Rrna Gene Sequencing

AbstractThe intestinal microbiota contributes to host metabolism and health. This study aimed to assess the effects of biochar on cecal microbiome-related metabolic changes in rats. Rats were orally administered rice straw biochar (RSB) at 1120 mg/kg body weight for 5 weeks. Cecal samples were analyzed to perform metabolic and microbial profiling via a combination of 16S rRNA gene sequencing and LC/MS techniques. We observed a significant influence of RSB in shaping the cecal bacterial community, including some potentially beneficial members of phylum Firmicutes belonging to unclassified Lachnospiraceae, Oscillibacter, and Clostridium XlVa and IV, as well as the depletion of some opportunistic pathogens belonging to Prevotella, Bacteroides and Paraprevotella. The metabolomic analysis revealed distinct changes in the cecal metabolic phenotype, including lower levels of L-isoleucine, indole-3-acetic acid, benzoic acid, and tetradecanoic acid as well as higher levels of L-phenylalanine, L-glutamate, 3-phenylpropanoic acid, chenodeoxycholic acid, cholic acid, 7-dehydrocholesterol, (5Z, 8Z, 11Z, 14Z, 17Z)-eicosapentaenoic acid, 11-deoxycorticosterone and retinol, which are mainly involved in the metabolic pathways of linoleic acid, amino acid and steroid hormone biosynthesis. Correlation analysis revealed a positive association of unclassified Lachnospiraceae, Oscillibacter and Clostridium IV with 3-phenylpropanoic acid, L-phenylalanine, L-glutamate, 11-deoxycorticosterone and 7-dehydrocholesterol. These results confirm that the gut microbiome is altered and may be critical for good performance under RSB application by interacting with metabolism.

scholarly journals Cultivable Microbial Diversity in Speleothems Using MALDI-TOF Spectrometry and DNA Sequencing from Krem Soitan, Krem Lawbah, Krem Mawpun, Khasi Hills, Meghalaya, India

2021 ◽  
Author(s):  
Mudgil Devender ◽  
Dhiraj Paul ◽  
Sushmitha Baskar ◽  
Ramanathan Baskar ◽  
Yogesh S Shouche
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Diversity ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Bacterial Isolates ◽  
Maldi Tof ◽  
Rrna Gene Sequencing ◽  
Culture Dependent

Abstract This study reports on the culturable microbial communities in caves from the Indian sub-continent. A high bacterial diversity and a greater bacterial taxonomic diversity is reported using MALDI-TOF spectrometry and 16S rRNA gene sequencing. This approach helped to detect a number bacterial strains from the Indian caves. The microbial diversity in the Indian caves is inadequately characterized. The study aims to expand the current understanding of bacterial diversity in the speleothems from Krem Soitan, Krem Lawbah, Krem Mawpun in Khasi Hills, Meghalaya, India. High microbial enumerations were observed on dilute nutrient agar (5.3 × 103 to 8.8 × 105) followed by M9 minimal medium (4 × 104 to 1.7 × 105) and R2A medium (1.0 × 104 to 5.7 × 105). A total of 826 bacterial isolates were selected and preserved for the study. 295 bacterial isolates were identified using MALDI-TOF spectrometry and the isolates which showed no reliable peaks were further identified by 16S rRNA gene sequencing. 91% of the total bacterial diversity was dominated by Proteobacteria and Actinobacteria. The other important phyla detected include the Firmicutes (7.45%), Deinococcus-Thermus (0.33%) and Bacteroidetes (0.67%). At the genus level, Pseudomonas (55%) and Arthrobacter (23%) were ubiquitous followed by Acinetobacter, Bacillus, Brevundimonas, Deinococcus, Flavobacterium, Paenibacillus, Pseudarthrobacter. Multivariate statistical analysis indicated that the bacterial genera formed separate clusters depending on the geochemical constituents in the spring waters suitable for their growth and metabolism. A culture-dependent approach was employed for elucidating the community structure colonizing the speleothems and wall deposits in the caves using MALDI-TOF and 16S rRNA gene sequencing. To the best of our knowledge, there are no previous geomicrobiological investigations in these caves and this study is a pioneering culture dependent study of the microbial community with many cultured isolates.

scholarly journals Bacterial growth in saturated and eutectic solutions of magnesium sulphate and potassium chlorate with relevance to Mars and the ocean worlds

2019 ◽  
Vol 18 (6) ◽  
pp. 502-509 ◽  
Author(s):  
Jonathan M. Wilks ◽  
Fei Chen ◽  
Benton C. Clark ◽  
Mark A. Schneegurt
Keyword(s):  
Microbial Growth ◽  
Freezing Point ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Bacterial Isolates ◽  
Near Surface ◽  
Iron Sulphate ◽  
High Concentrations ◽  
Rrna Gene Sequencing ◽  
Hygroscopic Salts

AbstractLiquid water on Mars might be created by deliquescence of hygroscopic salts or by permafrost melts, both potentially forming saturated brines. Freezing point depression allows these heavy brines to remain liquid in the near-surface environment for extended periods, perhaps as eutectic solutions, at the lowest temperatures and highest salt concentrations where ices and precipitates do not form. Perchlorate and chlorate salts and iron sulphate form brines with low eutectic temperatures and may persist under Mars near-surface conditions, but are chemically harsh at high concentrations and were expected to be incompatible with life, while brines of common sulphate salts on Mars may be more suitable for microbial growth. Microbial growth in saturated brines also may be relevant beyond Mars, to the oceans of Ceres, Enceladus, Europa and Pluto. We have previously shown strong growth of salinotolerant bacteria in media containing 2M MgSO4 heptahydrate (~50% w/v) at 25°C. Here we extend those observations to bacterial isolates from Basque Lake, BC and Hot Lake, WA, that grow well in saturated MgSO4 medium (67%) at 25°C and in 50% MgSO4 medium at 4°C (56% would be saturated). Psychrotolerant, salinotolerant microbes isolated from Basque Lake soils included Halomonas and Marinococcus, which were identified by 16S rRNA gene sequencing and characterized phenetically. Eutectic liquid medium constituted by 43% MgSO4 at −4°C supported copious growth of these psychrotolerant Halomonas isolates, among others. Bacterial isolates also grew well at the eutectic for K chlorate (3% at −3°C). Survival and growth in eutectic solutions increases the possibility that microbes contaminating spacecraft pose a contamination risk to Mars. The cold brines of sulphate and (per)chlorate salts that may form at times on Mars through deliquescence or permafrost melt have now been demonstrated to be suitable microbial habitats, should appropriate nutrients be available and dormant cells become vegetative.

The identification and genetic diversity of endophytic bacteria isolated from selected crops

2018 ◽  
Vol 156 (4) ◽  
pp. 547-556 ◽  
Author(s):  
M. Woźniak ◽  
A. Gałązka ◽  
J. Grządziel ◽  
M. Głodowska
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
Agricultural Soils ◽  
16S Rrna Gene Sequencing ◽  
Genomic Diversity ◽  
Wild Plants ◽  
Rrna Gene ◽  
Bacterial Isolates ◽  
Gradient Gel Electrophoresis ◽  
Rrna Gene Sequencing ◽  
Degree Of Differentiation

AbstractA collection of 45 isolates was created based on bacteria isolated from maize, broad bean, wheat, rye and wild plants such as horsetail and burdock. The aim of the current study was to isolate the bacteria, and then identify and assess the degree of genomic diversity. The molecular identification of microsymbionts isolated from the endosphere (root and stem) of plants grown in agricultural soils was performed using 16S rRNA gene sequencing. To evaluate the genomic diversity between strains that occurred in multiple host plants, 18 bacterial isolates representing four species were subjected to denaturing gradient gel electrophoresis. The 16S rDNA analysis assigned all bacterial isolates to ten genera, from whichRhizobiumwas represented by 19 isolates,Delftiaby 11,Agrobacteriumby five,Stenotrophomonasby three,Brevundimonasby two andNovosphingobium,Variovorax, Collimonas, AchromobacterandComamonasby only one isolate. Furthermore, the genomic diversity of the 11 isolates ofDelftiasp. was assessed using the BOX – polymerase chain reaction (BOX-PCR) and enterobacterial repetitive intergenic consensus – PCR (ERIC-PCR) methods. Typing patterns and analysis using BOX-PCR and ERIC-PCR data demonstrated similarities among the tested isolates. In general, the results obtained with BOX-PCR and ERIC-PCR were in good agreement. However, a greater degree of differentiation patterns of the genomic DNA was obtained in the ERIC-PCR method.

scholarly journals Bacterial isolates from bryozoan Pleurocodonellina sp.: Diversity and antimicrobial potential against pathogenic bacteria

2019 ◽  
Vol 20 (9) ◽  
Author(s):  
Meezan Ardhanu Asagabaldan ◽  
Gilles Bedoux ◽  
Nathalie Bourgougnon ◽  
Rhesi Kristiana ◽  
Diah Ayuningrum ◽  
...  
Keyword(s):  
Pathogenic Bacteria ◽  
16S Rrna Gene Sequencing ◽  
Antibacterial Activities ◽  
Multidrug Resistant ◽  
Rrna Gene ◽  
Bacterial Isolates ◽  
Bacterial Strains ◽  
Associated Bacteria ◽  
Antimicrobial Potential ◽  
Rrna Gene Sequencing

Abstract. Asagabaldan MA, Bedoux G, Bourgougnon N, Kristiana R, Ayuningrum D, Sabdono A, Trianto A, Radjasa OK. 2019. Bacterial isolates from bryozoan Pleurocodonellina sp.: Diversity and antimicrobial potential against pathogenic bacteria. Biodiversitas 20: 2528-2535.  There is an urgent need to discover new compounds with antibacterial activity, which can be developed into lead structures for the treatment of human disease caused by multidrug-resistant (MDR) bacteria. In this study, we focussed on bryozoan-associated bacteria to screen them toward antibacterial activities, since the microbiome of these organisms can still be regarded as under-investigated. Most of the few publications about bryozoan-associated bacteria focused on taxonomy and the potential as producers of antibacterial natural products were neglected. Four specimens of bryozoan Pleurocodonellina sp. were collected from Teluk Awur, Jepara in Java Sea, Indonesia. Therefrom, 56 bacterial strains were isolated, and 17 displayed antibacterial activities against MDR bacteria Pseudomonas aruginosa, Klebsiella pneumoniae, Acinetobacter baumannii, Enterobacter cloacae, and methicillin-resistant Staphylococcus aureus (MRSA). Taxonomic identification of the bacteria by 16S rRNA gene sequencing revealed them belonging to the genera Virgibacillus, Pseudoalteromonas, Halomonas, and Bacillus. Most interestingly, the genus Virgibacillus was dominantly obtained from the Pleurocodonellina sp. specimens, i.e., 12 active isolates. Nevertheless, the best activities against MDR bacteria (both Gram-positive and Gram-negative) were contributed to isolates showing >99% identity to Pseudoalteromonas. The results further suggest adding the genus Virgibacillus as bacteria associated with bryozoan, since to the best of our knowledge there were no reports of this genus isolated from bryozoan.

scholarly journals Molecular Detection and Identification of Bacteria in Urine Samples of Asymptomatic and Symptomatic Pregnant Women by 16S rRNA Gene Sequencing

2020 ◽  
Vol 15 (3) ◽  
Author(s):  
Pragya Lakshmi ◽  
Alok Bharadwaj ◽  
Ranjan Kumar Srivastava
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Tree ◽  
Pregnant Women ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Bacterial Isolates ◽  
Blast Analysis ◽  
Rrna Gene Sequencing

Objectives: The purpose of this study was to identify bacteria in urine samples of pregnant women of asymptomatic and symptomatic women by 16S rRNA gene sequencing. This study aims to identify different strains of microbes causing urinary tract infection (UTI). Methods: In the semi-quantitative culture technique, bacterial isolates such as Escherichia coli, Klebsiella, Pseudomonas, Staphylococcus, Coagulase-negative Staphylococcus, and Proteus were subjected to 16S rRNA gene sequencing followed by BLAST analysis and phylogenetic tree formation. The 16S rRNA gene sequencing was carried out to identify the specific strains of bacteria causing UTI. Results: According to the BLAST analysis, sample 1 revealed a 100% similarity to E. coli strain U5/41. Likewise, samples 2, 3, 4, 5 and 6 exhibited a 100% similarity to Klebsiella aerogenes strain F26, Pseudomonas entomophila strain 2014, Staphylococcus aureus strain NCTC13616, Staphylococcus saprophyticus strain FDAARGOS_355, Proteus mirabilis strain NCTC 11938, respectively. Conclusions: Six bacterial isolates were analyzed by 16S RNA gene sequencing followed by the construction of a phylogenetic tree construction up to the species level. This method was a valuable tool for cost-effective and accurate diagnosis of an array of uropathogens in both asymptomatic and symptomatic pregnant women.

scholarly journals Insights into the diversity and survival strategies of soil bacterial isolates from the Atacama Desert

2020 ◽  
Author(s):  
Alicyn Reverdy ◽  
Daniel Hathaway ◽  
Jessica Jha ◽  
Gabriel Michaels ◽  
Jeffrey Sullivan ◽  
...  
Keyword(s):  
16S Rrna ◽  
Antibiotic Production ◽  
Atacama Desert ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Soil Samples ◽  
Survival Strategies ◽  
Rrna Gene ◽  
Bacterial Isolates ◽  
Rrna Gene Sequencing

AbstractThe Atacama Desert, the driest and oldest desert in the world, is a hostile environment for life. Despite the inhospitable conditions, bacterial sequences detected in this location suggest rich bacterial life. This study tested the idea that certain bacteria would thrive in this location and that some of them could be cultivated permitting further characterization. Environmental surface soil samples from 1-5 cm deep were collected from 18 diverse locations within the Atacama Desert. To assess the bacterial taxa, diversity, and abundance, Illumina 16S rRNA gene sequencing was performed directly on soil samples. Bacteria were also cultured from the samples. We have a collection of 74 unique bacterial isolates after cultivation and confirmation by 16S rRNA gene sequencing. Pigmentation, biofilm formation, antibiotic production against Escherichia coli MG1655 and Staphylococcus aureus HG003, and antibiotic resistance were assessed on these isolates. We found that approximately a third of the colonies produced pigments, 80% of isolates formed biofilms, many isolates had antibiotic activity against E. coli and/or S. aureus, and many were resistant to commercial antibiotics. The functional characterization of these isolates gives us insight into the adaptive bacterial strategies in harsh environments and enables us to learn about their possible use in agriculture, healthcare, or biotechnology.Originality-Significant StatementThis study provides the first microbial diversity analysis from Atacama Desert soil, presents the cultivation and isolation of 74 unique bacterial isolates, many of which may be novel genera and species, and explores pigment production, antibiotic production and resistance, and unique biofilm development as bacterial survival strategies for living within extreme environments.

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