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Finding novel genes in bacterial communities isolated from the environment

L. Krause, N. N. Diaz, D. Bartels, R. A. Edwards, A. Puhler, F. Rohwer, F. Meyer, J. Stoye
2006 Bioinformatics  
Results: We introduce a novel gene finding algorithm that incorporates features overcoming the short length of the assembled contigs from environmental data, in-frame stop codons as well as frame shifts  ...  contained in bacterial sequences.  ...  We thank Beltran Rodriguez-Brito for generating the environmental data. NND was supported by the Deutscher Akademischer Austausch Dienst.  ... 
doi:10.1093/bioinformatics/btl247 pmid:16873483 fatcat:yyw2aeewnneafj24oxfzxjgjri

Metagenomic Approach towards Bioprospection of Novel Biomolecule(s) and Environmental Bioremediation

Manikant Tripathi, Durgesh Singh, Surendra Vikram, Vijay Singh, Shailendra Kumar
2018 Annual Research & Review in Biology  
The scanty information about the factors governing the microbial growth within stressed ARRB, 22(2): 1-12, 2018; Article no.ARRB.38385 2 environments is the major constraint in the recovery of novel biomolecule  ...  (s) from extreme habitats.  ...  The worms transport hydrogen sulfide and CO 2 from environment to the bacterial symbiont.  ... 
doi:10.9734/arrb/2018/38385 fatcat:u3yazwprvvbsjobvasnk2coibq

Microbial Community Analysis in the Roots of Aquatic Plants and Isolation of Novel Microbes Including an Organism of the Candidate Phylum OP10

Yasuhiro Tanaka, Hideyuki Tamaki, Hiroaki Matsuzawa, Masahiro Nigaya, Kazuhiro Mori, Yoichi Kamagata
2012 Microbes and Environments  
In comparisons of microbial communities between the plant roots and pond water taken from near the plants, the microbial diversity in the plant roots (e.g. 4.40-4.26 Shannon-Weiner index) were higher than  ...  More importantly, compared to pond water, we succeeded in isolating approximately two times more novel isolate phylotypes, including a bacterium of candidate phylum OP10 (recently named Armatimonadetes  ...  We thank Yamanashi Prefectural Wood Park at Kanegawa and the Society for the Research of Pro-Natural Civil Engineering Method of Yamanashi for their help in the cultivation of aquatic plants.  ... 
doi:10.1264/jsme2.me11288 pmid:22791047 pmcid:PMC4036017 fatcat:4ylruz5uyndobgs4uarpwayvde

Insights into novel antimicrobial compounds and antibiotic resistance genes from soil metagenomes

Alinne P. de Castro, Gabriel da R. Fernandes, Octávio L. Franco
2014 Frontiers in Microbiology  
In this context, this review will focus on resistance genes as well as on novel antibiotics revealed by a metagenomics approach from the soil environment.  ...  As an alternative, metagenomics has been used as a reliable approach to reveal the prospective reservoir of antimicrobial compounds and antibiotic resistance genes in the uncultured microbial community  ...  Metagenomics has also been considered a promising approach for the isolation of unusual antibiotics from environmental samples, as well as in identifying the mechanisms of bacterial resistance in the in  ... 
doi:10.3389/fmicb.2014.00489 pmid:25278933 pmcid:PMC4166954 fatcat:hapkjtxwxvggpkt5l6w3fyjo4e

Adaptation in Natural Microbial Populations

Britt Koskella, Michiel Vos
2015 Annual Review of Ecology, Evolution and Systematics  
In the first case, bacterial recombination resembles gene conversion in eukaryotes, and results in the creation of novel combinations of mutations.  ...  One nice illustration of how changes in species abundances in a community co-occur with changes in gene abundances within species in the community in response 15 to environmental perturbation can be found  ... 
doi:10.1146/annurev-ecolsys-112414-054458 fatcat:wlspdoboxbgktd3wdaaanw547i

Rediscovery of the Microbial World in Microbial Ecology

Shin Haruta
2013 Microbes and Environments  
Craig Everroad for careful English review of the manuscript.  ...  Diene et al. found a novel species of fungi from soils by cultivation and isolation (5).  ...  Analysis of community-level responses against disturbance or change in environmental parameters is a practical approach to find out the key members and interspecies relationships within microbial communities  ... 
doi:10.1264/jsme2.me2803rh pmid:24064954 pmcid:PMC4070962 fatcat:vvjtg537sfdw7j6kzq3fddt3um

Reporting Key Features in Cold-Adapted Bacteria

Paula Tribelli, Nancy López
2018 Life  
In addition, metagenomic, metatranscriptomic and metaproteomic data are used to detect key functions in bacterial communities inhabiting cold environments.  ...  It is well known that cold environments are predominant over the Earth and there are a great number of reports analyzing bacterial adaptations to cold.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/life8010008 pmid:29534000 pmcid:PMC5871940 fatcat:xtwrvmsa4bd35bz6uwuc6pe7bi

Comparative Analysis of Microbial Communities in Fronds and Roots of Three Duckweed Species: Spirodela polyrhiza, Lemna minor, and Lemna aequinoctialis

Tomoki Iwashita, Yasuhiro Tanaka, Hideyuki Tamaki, Yasuko Yoneda, Ayaka Makino, Yuka Tateno, Yan Li, Tadashi Toyama, Yoichi Kamagata, Kazuhiro Mori
2020 Microbes and Environments  
The microbial compositions of the fronds were distinct from those of the roots in the three species.  ...  The microbial communities inhabiting the fronds of duckweeds have not been investigated in as much detail as those on the roots.  ...  Acknowledgements We are grateful to Yamanashi Prefectural Wood Park at Kanegawa and the Society for the Research of Pro-Natural Civil Engineering Method of Yamanashi 303 for their help with the cultivation  ... 
doi:10.1264/jsme2.me20081 pmid:32684532 pmcid:PMC7511783 fatcat:d4gfwjxtsnbarhda4z5j7ea3uq

Culturomics and metagenomics: In understanding of environmental resistome

Monika Nowrotek, Łukasz Jałowiecki, Monika Harnisz, Grażyna Anna Płaza
2019 Frontiers of Environmental Science and Engineering  
genes from environments.  ...  In this review, two omics methods, i.e. culturomics, a new approach, and metagenomics, used to study antibiotic resistance in environmental samples, are described.  ...  In this study, almost 1.5 Gbp of microbial sequences from three marine sites was recovered. This led to the finding of almost 70 thousand novel genes (Venter et al., 2004) .  ... 
doi:10.1007/s11783-019-1121-8 fatcat:rqt6vnh7vnh2hoxol43auyffce

Sampling Terrestrial Environments for Bacterial Polyketides

Patrick Hill, Graham Heberlig, Christopher Boddy
2017 Molecules  
the environment.  ...  This review summarizes for the bioprospector the state-of-the-field in terrestrial microbial ecology.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/molecules22050707 pmid:28468277 fatcat:dpzohcv34fa6bgi6fp36j5lvoi

Analysis of bacterial diversity associated with polyketide synthase (PKS) gene in brackish metagenome of TsoKar Lake of Ladakh, India

V. K. Gupta, School of Biotechnology, Shri Mata Vaishno Devi University, Katra - 182 320, India, S.S. Khan, V. Verma, S. Rasool, School of Biotechnology, Shri Mata Vaishno Devi University, Katra - 182 320, India, School of Biotechnology, Shri Mata Vaishno Devi University, Katra - 182 320, India, School of Biotechnology, Shri Mata Vaishno Devi University, Katra - 182 320, India
2020 Journal of environmental biology  
Aim: Methodology: Results: Interpretation: Keywords: To explore bacterial diversity associated to polyketide synthase (PKS) genes in the TsoKar brackish metagenome.  ...  The results of this study confirm that this unique niche harbors good bacterial diversity associated with polyketide synthase genes, which justifies the idea of bioprospecting such niches for the discovery  ...  and mining novel hydrolases from brackish water lakes of Ladakh region by metagenomic approach".  ... 
doi:10.22438/jeb/41/4/mrn-1331 fatcat:qjwqhjh4dzf2bkhc7ruhwkujpm

Ecological and Temporal Constraints in the Evolution of Bacterial Genomes

Luis Boto, Jose Luis Martínez
2011 Genes  
In particular, we review how the different processes contribute to evolution in microbial communities, in free-living bacteria or in bacteria living in isolation.  ...  In addition, we discuss the temporal constraints in the evolution of bacterial genomes, considering bacterial evolution from the perspective of processes of short-sighted evolution and punctual acquisition  ...  Author's laboratories are supported by grants BIO2008-00090 from the Spanish Ministry of Science and Innovation, CGL 2010-15231 from Spanish DGI and KBBE-227258 (BIOHYPO), HEALTH-F3-2010-241476 (PAR) and  ... 
doi:10.3390/genes2040804 pmid:24710293 pmcid:PMC3927597 fatcat:z6r77voj3fcbbfhwpchlrcrhpq

Phylogeography of the Bradyrhizobium spp. Associated With Peanut, Arachis hypogaea: Fellow Travelers or New Associations?

Besma Bouznif, Ibtissem Guefrachi, Ricardo C. Rodríguez de la Vega, Mariangela Hungria, Mohamed Mars, Benoit Alunni, Jacqui Anne Shykoff
2019 Frontiers in Microbiology  
symbionts, or whether they acquired their current associations de novo from the bacterial community within the area of introduction.  ...  strains isolated from peanut roots across the areas of peanut cultivation.  ...  the abiotic environment to be acquired from the local bacterial community at the site of introduction.  ... 
doi:10.3389/fmicb.2019.02041 pmid:31551977 pmcid:PMC6737463 fatcat:csboov6v2jhajeedvsjxuhwiuu

The Use of Metagenomic Approaches to Analyze Changes in Microbial Communities

Girish Neelakanta, Hameeda Sultana
2013 Microbiology Insights  
In this study, we highlight recent advances in the field of metagenomics for analyzing microbial communities in different ecosystems ranging from oceans to the human microbiome.  ...  In summary, we provide a snapshot for the recent advances in metagenomics approach for analyzing changes in the microbial communities in different ecosystems.  ...  enormous potential of soil metagenomics in isolating novel classes of genes.  ... 
doi:10.4137/mbi.s10819 pmid:24826073 pmcid:PMC3987754 fatcat:erfq5zzrpfgedb6rrarddedpdu

Diversity of bacteria from Antarctica, Arctic, Himalayan glaciers and Stratosphere

Sisinthy Shivaji, Madhab K Chattopadhyay, Gundlapally S Reddy
2019 Proceedings of the Indian National Science Academy  
A major part of the review includes studies carried by scientists in India in the above extreme cold habitats.  ...  It also establishes their utility to mankind in the spheres of health, agriculture and medicine.  ...  The multistress-protective potential of these molecules could find application in construction of genetically engineered sturdy bacterial strains, suitable for bioremediation in harsh environments.  ... 
doi:10.16943/ptinsa/2019/49717 fatcat:r7armjenibdftev5ztc7nhxcci
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