scholarly journals Metagenomics: Retrospect and Prospects in High Throughput Age

2015 ◽  
Vol 2015 ◽  
pp. 1-13 ◽  
Author(s):  
Satish Kumar ◽  
Kishore Kumar Krishnani ◽  
Bharat Bhushan ◽  
Manoj Pandit Brahmane
Keyword(s):  
Community Dynamics ◽  
Full Potential ◽  
Basic Study ◽  
Independent Manner ◽  
Microbial Community Dynamics ◽  
Current State ◽  
Culture Independent ◽  
Almost All ◽  
Insight Into ◽  
Generation Sequencing

In recent years, metagenomics has emerged as a powerful tool for mining of hidden microbial treasure in a culture independent manner. In the last two decades, metagenomics has been applied extensively to exploit concealed potential of microbial communities from almost all sorts of habitats. A brief historic progress made over the period is discussed in terms of origin of metagenomics to its current state and also the discovery of novel biological functions of commercial importance from metagenomes of diverse habitats. The present review also highlights the paradigm shift of metagenomics from basic study of community composition to insight into the microbial community dynamics for harnessing the full potential of uncultured microbes with more emphasis on the implication of breakthrough developments, namely, Next Generation Sequencing, advanced bioinformatics tools, and systems biology.

scholarly journals Microbial community dynamics during alfalfa silage with or without clostridial fermentation

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Rongrong Li ◽  
Di Jiang ◽  
Mingli Zheng ◽  
Pengjiao Tian ◽  
Menghu Zheng ◽  
...  
Keyword(s):  
Microbial Community ◽  
Next Generation Sequencing ◽  
Bacterial Communities ◽  
Community Dynamics ◽  
Ammonia Nitrogen ◽  
Clostridium Tyrobutyricum ◽  
Microbial Community Dynamics ◽  
Vigorous Growth ◽  
Alfalfa Silage ◽  
Generation Sequencing

Abstract This study was conducted to examine the effects of Lactobacillus plantarum (LP) and sucrose (S) on clostridial community dynamics and correlation between clostridia and other bacteria in alfalfa silage during ensiling. Fresh alfalfa was directly ensiled without (CK) or with additives (LP, S, LP + S) for 7, 14, 28 and 56 days. Clostridial and bacterial communities were evaluated by next-generation sequencing. Severe clostridial fermentation occurred in CK, as evidenced by the high contents of butyric acid, ammonia nitrogen, and clostridia counts, whereas all additives, particularly LP + S, decreased silage pH and restrained clostridial fermentation. Clostridium perfringens and Clostridium butyricum might act as the main initiators of clostridial fermentation, with Clostridium tyrobutyricum functioning as the promoters of fermentation until the end of ensiling. Clostridium tyrobutyricum (33.5 to 98.0%) dominated the clostridial community in CK from 14 to 56 days, whereas it was below 17.7% in LP + S. Clostridium was negatively correlated with the genus Lactobacillus, but positively correlated with the genera Enterococcus, Lactococcus and Leuconostoc. Insufficient acidification promoted the vigorous growth of C. tyrobutyricum of silage in later stages, which was mainly responsible for the clostridial fermentation of alfalfa silage.

scholarly journals Translating Lung Microbiome Profiles into the Next-Generation Diagnostic Gold Standard for Pneumonia: a Clinical Investigator’s Perspective

mSystems ◽  
2018 ◽  
Vol 3 (2) ◽  
Author(s):  
Georgios D. Kitsios
Keyword(s):  
Pulmonary Infections ◽  
Next Generation ◽  
Clinical Validity ◽  
Lung Microbiome ◽  
Current State ◽  
Incubation Periods ◽  
Culture Independent ◽  
Diagnostic Approaches ◽  
Microbial Dna ◽  
Generation Sequencing

ABSTRACT Severe bacterial pneumonia is a major global cause of morbidity and mortality, yet current diagnostic approaches rely on identification of causative pathogens by cultures, which require extended incubation periods and often fail to detect relevant pathogens. Consequently, patients are prescribed broad-spectrum antibiotics in a “one-size-fits-all” manner, which may be inappropriate for their individual needs and promote antibiotic resistance. My research focuses on leveraging next-generation sequencing of microbial DNA directly from patient samples for the development of new, culture-independent definitions of pneumonia. In this perspective article, I discuss the current state of the field and focus on the conceptual and research design challenges for clinical translation. With ongoing technological advancements and application of computational biology methods for assessing clinical validity and utility, I anticipate that sequencing-based diagnostics will soon be able to positively disrupt the way we think about, diagnose, and treat pulmonary infections.

scholarly journals Ecosystem Resilience and Limitations Revealed by Soil Bacterial Community Dynamics in a Bark Beetle-Impacted Forest

mBio ◽  
2017 ◽  
Vol 8 (6) ◽  
Author(s):  
Kristin M. Mikkelson ◽  
Brent M. Brouillard ◽  
Chelsea M. Bokman ◽  
Jonathan O. Sharp
Keyword(s):  
Water Quality ◽  
Bacterial Community ◽  
Tree Mortality ◽  
Community Dynamics ◽  
Watershed Scale ◽  
Microbial Community Dynamics ◽  
Local Soil ◽  
The World ◽  
Water Quality And Quantity ◽  
Insight Into

ABSTRACT Forested ecosystems throughout the world are experiencing increases in the incidence and magnitude of insect-induced tree mortality with large ecologic ramifications. Interestingly, correlations between water quality and the extent of tree mortality in Colorado montane ecosystems suggest compensatory effects from adjacent live vegetation that mute responses in less severely impacted forests. To this end, we investigated whether the composition of the soil bacterial community and associated functionality beneath beetle-killed lodgepole pine was influenced by the extent of surrounding tree mortality. The most pronounced changes were observed in the potentially active bacterial community, where alpha diversity increased in concert with surrounding tree mortality until mortality exceeded a tipping point of ~30 to 40%, after which diversity stabilized and decreased. Community structure also clustered in association with the extent of surrounding tree mortality with compositional trends best explained by differences in NH4 + concentrations and C/N ratios. C/N ratios, which were lower in soils under beetle-killed trees, further correlated with the relative abundance of putative nitrifiers and exoenzyme activity. Collectively, the response of soil microorganisms that drive heterotrophic respiration and decay supports observations of broader macroscale threshold effects on water quality in heavily infested forests and could be utilized as a predictive mechanism during analogous ecosystem disruptions. IMPORTANCE Forests around the world are succumbing to insect infestation with repercussions for local soil biogeochemistry and downstream water quality and quantity. This study utilized microbial community dynamics to address why we are observing watershed scale biogeochemical impacts from forest mortality in some impacted areas but not others. Through a unique “tree-centric” approach, we were able to delineate plots with various tree mortality levels within the same watershed to see if surviving surrounding vegetation altered microbial and biogeochemical responses. Our results suggest that forests with lower overall tree mortality levels are able to maintain “normal” ecosystem function, as the bacterial community appears resistant to tree death. However, surrounding tree mortality influences this mitigating effect with various linear and threshold responses whereupon the bacterial community and its function are altered. Our study lends insight into how microscale responses propagate upward into larger-scale observations, which may be useful for future predictions during analogous disruptions. IMPORTANCE Forests around the world are succumbing to insect infestation with repercussions for local soil biogeochemistry and downstream water quality and quantity. This study utilized microbial community dynamics to address why we are observing watershed scale biogeochemical impacts from forest mortality in some impacted areas but not others. Through a unique “tree-centric” approach, we were able to delineate plots with various tree mortality levels within the same watershed to see if surviving surrounding vegetation altered microbial and biogeochemical responses. Our results suggest that forests with lower overall tree mortality levels are able to maintain “normal” ecosystem function, as the bacterial community appears resistant to tree death. However, surrounding tree mortality influences this mitigating effect with various linear and threshold responses whereupon the bacterial community and its function are altered. Our study lends insight into how microscale responses propagate upward into larger-scale observations, which may be useful for future predictions during analogous disruptions.

Rare unclassified 16S rRNA operational taxonomic units from the uncharted Engaño Bay (Argentinean Patagonia)

2018 ◽  
Vol 64 (1) ◽  
pp. 91-96
Author(s):  
Andrea Y. Calvo ◽  
Julieta M. Manrique ◽  
Leandro R. Jones
Keyword(s):  
16S Rrna ◽  
Community Dynamics ◽  
Sequence Data ◽  
River Estuary ◽  
Fragmented Habitats ◽  
Operational Taxonomic Units ◽  
Microbial Community Dynamics ◽  
Argentinean Patagonia ◽  
Culture Independent ◽  
Taxonomic Assignments

Rare microbes make up most of the diversity of marine microbiomes, and recent works have highlighted their importance for microbial community dynamics and in fragmented habitats. Rare taxa have been infrequently studied in comparison with abundant groups, and rare unclassified sequences are common in culture-independent studies. Here, we describe a detailed analysis of nonclassifiable sequences from the Chubut river estuary at the Argentinean Patagonia. Standard taxonomic assignments of environmental 16S rRNA sequences resulted in about 13% unclassified operational taxonomic units (OTUs). The potential affiliations of these OTUs could be narrowed by mapping the classification software assignments on a phylogeny obtained directly from our environmental sequence data. Customized BLAST analyses were remarkably consistent with these phylogenetic assignments, especially when the unclassified OTUs were blasted against sequences from cultured and type microorganisms. In addition, our BLAST analyses revealed significant similarities between several unclassified OTUs and a plethora of unclassified sequences from around the world. Further phylogenetic comparisons with 6194 carefully selected reference sequences showed that these unclassified sequences may correspond to 5 unnamed groups, possibly encompassing ranks from subclass to family inside the Alphaproteobacteria, and to an unknown Gracilibacteria lineage. Overall, these results demonstrate the value of straight phylogenetic analysis, customized BLAST searches, and comparisons with sequences from type material, for the systematic study of rare unclassified sequences.

scholarly journals Resolving challenges in quantitative modeling of microbial community dynamics

2018 ◽  
Author(s):  
Samuel F. M. Hart ◽  
Hanbing Mi ◽  
Robin Green ◽  
Li Xie ◽  
Jose Mario Bello Pineda ◽  
...  
Keyword(s):  
Community Dynamics ◽  
Rapid Evolution ◽  
Model Performance ◽  
Experimental Results ◽  
Model Parameters ◽  
Microbial Community Dynamics ◽  
Improve Model ◽  
Measured Strain ◽  
Community Environments ◽  
Almost All

AbstractMicrobial communities can perform biochemical activities that monocultures cannot. Controlling communities requires an understanding of community dynamics. Here, we mathematically predict the growth rate of an engineered community consisting of two S. cerevisiae strains, each releasing a metabolite required and consumed by the partner. Initial model parameters were based on strain phenotypes measured in batch mono-cultures with zero or excess metabolite, and failed to quantitatively predict experimental results. To resolve model-experiment discrepancy, we chemically identified the correct exchanged metabolites, but this did not improve model performance. We then re-measured strain phenotypes in chemostats mimicking the metabolite-limited community environments, while mitigating or incorporating effects of rapid evolution. Almost all phenotypes we measured varied significantly with the metabolite environment. Once we used parameters measured in community-like chemostat environments, prediction agreed with experimental results. In summary, using a simplified community, we uncovered, and devised means to resolve, modeling challenges that are likely general.

scholarly journals Microbial diversity of the Arabian Sea in the Oxygen minimum zones by metagenomics approach

2019 ◽  
Author(s):  
Mandar S. Paingankar ◽  
Kedar Ahire ◽  
Pawan Mishra ◽  
Shriram Rajpathak ◽  
Deepti D. Deobagkar
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Arabian Sea ◽  
Community Dynamics ◽  
Oxygen Depletion ◽  
Oxygen Minimum Zones ◽  
Microbial Community Dynamics ◽  
Nitrate Reducers ◽  
Insight Into ◽  
Oxygen Minimum

ABSTRACTLarge oxygen depleted areas known as oxygen minimum zones (OMZ) have been observed in the Arabian Sea and recent reports indicate that these areas are expanding at an alarming rate. In marine waters, oxygen depletion may also be related to global warming and the temperature rise, acidification and deoxygenation can lead to major consequences wherein the plants, fish and other biota will struggle to survive in the ecosystem.The current study has identified the microbial community structure using NGS based metagenomics analysis in the water samples collected at different depth from the oxygen depleted and non-OMZ areas of Arabian Sea. Environmental variables such as depth, site of collection and oxygen concentration appeared to influence the species richness and evenness among microbial communities in these locations. Our observations clearly indicate that population dynamics of microbes consisting of nitrate reducers accompanied by sulphate reducers and sulphur oxidizers participate in the interconnected geochemical cycles of the OMZ areas. In addition to providing baseline data related to the diversity and microbial community dynamics in oxygen-depleted water in the OMZ; such analysis can provide insight into processes regulating productivity and ecological community structure of the ocean.

scholarly journals Diversity of Biodeteriorative Bacterial and Fungal Consortia in Winter and Summer on Historical Sandstone of the Northern Pergola, Museum of King John III’s Palace at Wilanow, Poland

2021 ◽  
Vol 11 (2) ◽  
pp. 620
Author(s):  
Magdalena Dyda ◽  
Agnieszka Laudy ◽  
Przemyslaw Decewicz ◽  
Krzysztof Romaniuk ◽  
Martyna Ciezkowska ◽  
...  
Keyword(s):  
Seasonal Changes ◽  
Microbial Community Composition ◽  
Fungal Communities ◽  
Bacterial Strains ◽  
Microbial Biodiversity ◽  
Acidophilic Bacteria ◽  
Almost All ◽  
Generation Sequencing ◽  
King John

The aim of the presented investigation was to describe seasonal changes of microbial community composition in situ in different biocenoses on historical sandstone of the Northern Pergola in the Museum of King John III’s Palace at Wilanow (Poland). The microbial biodiversity was analyzed by the application of Illumina-based next-generation sequencing methods. The metabarcoding analysis allowed for detecting lichenized fungi taxa with the clear domination of two genera: Lecania and Rhinocladiella. It was also observed that, during winter, the richness of fungal communities increased in the biocenoses dominated by lichens and mosses. The metabarcoding analysis showed 34 bacterial genera, with a clear domination of Sphingomonas spp. across almost all biocenoses. Acidophilic bacteria from Acidobacteriaceae and Acetobacteraceae families were also identified, and the results showed that a significant number of bacterial strains isolated during the summer displayed the ability to acidification in contrast to strains isolated in winter, when a large number of isolates displayed alkalizing activity. Other bacteria capable of nitrogen fixation and hydrocarbon utilization (including aromatic hydrocarbons) as well as halophilic microorganisms were also found. The diversity of organisms in the biofilm ensures its stability throughout the year despite the differences recorded between winter and summer.

Sign in / Sign up

Export Citation Format

Share Document