scholarly journals Multi-omic Characterization of Intraspecies Variation in Laboratory and Natural Environments

mSystems ◽  
2021 ◽  
Vol 6 (4) ◽  
Author(s):  
Megan G. Behringer
Keyword(s):  
Microbial Communities ◽  
Ecosystem Function ◽  
Interspecific Variation ◽  
Natural Environments ◽  
Species Relationships ◽  
Human Gut ◽  
Intraspecies Variation ◽  
Subglacial Lake

Investigation of microbial communities has led to many advances in our understanding of ecosystem function, whether that ecosystem is a subglacial lake or the human gut. Within these communities, much emphasis has been placed on interspecific variation and between-species relationships.

scholarly journals Outlier Detection for Minor Compositional Variations in Taxonomic Abundance Data

2019 ◽  
Vol 9 (7) ◽  
pp. 1355
Author(s):  
Koji Ishiya ◽  
Sachiyo Aburatani
Keyword(s):  
Microbial Communities ◽  
Natural Environments ◽  
Human Gut ◽  
Short Term ◽  
Computational Framework ◽  
Dietary Changes ◽  
Compositional Changes ◽  
Compositional Variations ◽  
Living Organisms ◽  
Shed Light

To understand the activities of complex microbial communities in various natural environments and living organisms, we need to capture the compositional changes in their taxonomic abundance. Here, we propose a new computational framework to detect compositional changes in microorganisms, including minor bacteria. This framework is designed to statistically assess relative variations in taxonomic abundance. By using this approach, we detected compositional changes in the human gut microbiome that might be associated with short-term human dietary changes. Our approach can shed light on the compositional changes of minor microorganisms that are easily overlooked.

scholarly journals MetaLab 2.0 enables accurate post-translational modifications profiling in metaproteomics

2019 ◽  
Author(s):  
Kai Cheng ◽  
Zhibin Ning ◽  
Xu Zhang ◽  
Leyuan Li ◽  
Bo Liao ◽  
...  
Keyword(s):  
Data Analysis ◽  
Microbial Communities ◽  
Search Strategy ◽  
Structure And Function ◽  
Research Field ◽  
Human Gut ◽  
Post Translational Modifications ◽  
Protein Functions ◽  
And Function

AbstractStudying the structure and function of microbiomes is an emerging research field. Metaproteomic approaches focusing on the characterization of expressed proteins and post-translational modifications (PTMs) provide a deeper understanding of microbial communities. Previous research has highlighted the value of examining microbiome-wide protein expression in studying the roles of the microbiome in human diseases. Nevertheless, the regulation of protein functions in complex microbiomes remains under-explored. This is mainly due to the lack of efficient bioinformatics tools to identify and quantify PTMs in the microbiome. We have developed a comprehensive software termed MetaLab for the data analysis of metaproteomic datasets. Here we build an open search workflow within MetaLab for unbiased identification and quantification of PTMs from microbiome samples. This bioinformatics platform provides information about proteins, PTMs, taxa, functions, and pathways of microbial communities. The performance of the workflow was evaluated using conventional proteomics, metaproteomics from mouse and human gut microbiomes, and modification-specific enriched datasets. Superior accuracy and sensitivity were obtained simultaneously by using our method comparing with the traditional closed search strategy.

scholarly journals Antimicrobial-resistance genes in the human gut prior the antibiotic-therapy era

2019 ◽  
Author(s):  
Tasha Santiago-Rodriguez
Keyword(s):  
Antibiotic Resistance ◽  
Antimicrobial Resistance ◽  
Antibiotic Therapy ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Natural Environments ◽  
Beta Lactams ◽  
Human Gut ◽  
Antimicrobial Resistance Genes

Antibiotic-resistance has long been associated with the use and abuse of antibiotics. However, increasing evidence is suggesting that antibiotic-resistance is in fact a phenomenon that has been occurring in natural environments for thousands and possibly millions of years. With the expansion of the microbiome field, it is now possible to characterize antibiotic-resistance genes altogether in different samples, including the human gut. This has also enabled the characterization of ancient human gut microbiomes, which also include antibiotic-resistance genes. Mummified gut remains represent a unique opportunity to characterize the microbiome and antibiotic-resistance genes prior the antibiotic-therapy era. Surprisingly, mummies from the Inca and Italian nobility cultures showed to possess antibiotic-resistance-like genes similar to modern-day antibiotic-resistance genes conferring resistance to beta-lactams, sulfa, quinolones and vancomycin, just to mention a few examples. This is intriguing as it further supports that antibiotic-resistance began in the environment and was transferred to the human gut by means that remain to be investigated and are a matter of ongoing speculation.

scholarly journals Bacterial diversity in the waterholes of the Kruger National Park: an eDNA metabarcoding approach

Genome ◽  
2019 ◽  
Vol 62 (3) ◽  
pp. 229-242 ◽  
Author(s):  
Maxwell J. Farrell ◽  
Danny Govender ◽  
Mehrdad Hajibabaei ◽  
Michelle van der Bank ◽  
T. Jonathan Davies
Keyword(s):  
Microbial Communities ◽  
Bacterial Diversity ◽  
Bacterial Communities ◽  
National Park ◽  
Kruger National Park ◽  
Baseline Survey ◽  
Natural Environments ◽  
Essential Components ◽  
Conservation Concern

Bacteria are essential components of natural environments. They contribute to ecosystem functioning through roles as mutualists and pathogens for larger species, and as key components of food webs and nutrient cycles. Bacterial communities respond to environmental disturbances, and the tracking of these communities across space and time may serve as indicators of ecosystem health in areas of conservation concern. Recent advances in DNA sequencing of environmental samples allow for rapid and culture-free characterization of bacterial communities. Here we conduct the first metabarcoding survey of bacterial diversity in the waterholes of the Kruger National Park, South Africa. We show that eDNA can be amplified from waterholes and find strongly structured microbial communities, likely reflecting local abiotic conditions, animal ecology, and anthropogenic disturbance. Over timescales from days to weeks we find increased turnover in community composition, indicating bacteria may represent host-associated taxa of large vertebrates visiting the waterholes. Through taxonomic annotation we also identify pathogenic taxa, demonstrating the utility of eDNA metabarcoding for surveillance of infectious diseases. These samples serve as a baseline survey of bacterial diversity in the Kruger National Park, and in the future, spatially distinct microbial communities may be used as markers of ecosystem disturbance, or biotic homogenization across the park.

scholarly journals Influence of pig farming on human Gut Microbiota: role of airborne microbial communities

Gut Microbes ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 1-13
Author(s):  
Julia Moor ◽  
Tsering Wüthrich ◽  
Suzanne Aebi ◽  
Nadezda Mostacci ◽  
Gudrun Overesch ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Microbial Communities ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Pig Farming

scholarly journals Metagenomic Characterization of Microbial Communities In Situ Within the Deeper Layers of the Ileum in Crohn’s Disease

2016 ◽  
Vol 2 (5) ◽  
pp. 563-566.e5 ◽  
Author(s):  
Chandra Sekhar Pedamallu ◽  
Ami S. Bhatt ◽  
Susan Bullman ◽  
Sharyle Fowler ◽  
Samuel S. Freeman ◽  
...  
Keyword(s):  
Crohn’S Disease ◽  
Crohn's Disease ◽  
Microbial Communities

scholarly journals Deconstruction of Lignin: From Enzymes to Microorganisms

Molecules ◽  
2021 ◽  
Vol 26 (8) ◽  
pp. 2299
Author(s):  
Jéssica P. Silva ◽  
Alonso R. P. Ticona ◽  
Pedro R. V. Hamann ◽  
Betania F. Quirino ◽  
Eliane F. Noronha
Keyword(s):  
Microbial Communities ◽  
Metabolic Pathways ◽  
Low Cost ◽  
Direct Analysis ◽  
Industrial Applications ◽  
Natural Environments ◽  
Lignocellulosic Residues ◽  
Complementary Techniques ◽  
Plant Polymer ◽  
Powerful Strategy

Lignocellulosic residues are low-cost abundant feedstocks that can be used for industrial applications. However, their recalcitrance currently makes lignocellulose use limited. In natural environments, microbial communities can completely deconstruct lignocellulose by synergistic action of a set of enzymes and proteins. Microbial degradation of lignin by fungi, important lignin degraders in nature, has been intensively studied. More recently, bacteria have also been described as able to break down lignin, and to have a central role in recycling this plant polymer. Nevertheless, bacterial deconstruction of lignin has not been fully elucidated yet. Direct analysis of environmental samples using metagenomics, metatranscriptomics, and metaproteomics approaches is a powerful strategy to describe/discover enzymes, metabolic pathways, and microorganisms involved in lignin breakdown. Indeed, the use of these complementary techniques leads to a better understanding of the composition, function, and dynamics of microbial communities involved in lignin deconstruction. We focus on omics approaches and their contribution to the discovery of new enzymes and reactions that impact the development of lignin-based bioprocesses.

scholarly journals Characterization of Ocular Surface Microbial Profiles Revealed Discrepancies between Conjunctival and Corneal Microbiota

Pathogens ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 405
Author(s):  
Anna Matysiak ◽  
Michal Kabza ◽  
Justyna A. Karolak ◽  
Marcelina M. Jaworska ◽  
Malgorzata Rydzanicz ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Ocular Surface ◽  
Molecular Techniques ◽  
Corneal Tissue ◽  
Rna Seq ◽  
Microbiome Composition ◽  
Viral Sequences ◽  
Pcr Techniques ◽  
Unmapped Reads

The ocular microbiome composition has only been partially characterized. Here, we used RNA-sequencing (RNA-Seq) data to assess microbial diversity in human corneal tissue. Additionally, conjunctival swab samples were examined to characterize ocular surface microbiota. Short RNA-Seq reads, obtained from a previous transcriptome study of 50 corneal tissues, were mapped to the human reference genome GRCh38 to remove sequences of human origin. The unmapped reads were then used for taxonomic classification by comparing them with known bacterial, archaeal, and viral sequences from public databases. The components of microbial communities were identified and characterized using both conventional microbiology and polymerase chain reaction (PCR) techniques in 36 conjunctival swabs. The majority of ocular samples examined by conventional and molecular techniques showed very similar microbial taxonomic profiles, with most of the microorganisms being classified into Proteobacteria, Firmicutes, and Actinobacteria phyla. Only 50% of conjunctival samples exhibited bacterial growth. The PCR detection provided a broader overview of positive results for conjunctival materials. The RNA-Seq assessment revealed significant variability of the corneal microbial communities, including fastidious bacteria and viruses. The use of the combined techniques allowed for a comprehensive characterization of the eye microbiome’s elements, especially in aspects of microbiota diversity.

scholarly journals Characterization of Unripe and Mature Avocado Seed Oil in Different Proportions as Phase Change Materials and Simulation of Their Cooling Storage

Molecules ◽  
2020 ◽  
Vol 26 (1) ◽  
pp. 107
Author(s):  
Evelyn Reyes-Cueva ◽  
Juan Francisco Nicolalde ◽  
Javier Martínez-Gómez
Keyword(s):  
Phase Change ◽  
Phase Change Materials ◽  
Seed Oil ◽  
Energy System ◽  
Maturity Stage ◽  
Natural Environments ◽  
Renewable Materials ◽  
Scanning Calorimetry ◽  
Avocado Seed

Environmental problems have been associated with energy consumption and waste management. A solution is the development of renewable materials such as organic phase change materials. Characterization of new materials allows knowing their applications and simulations provide an idea of how they can developed. Consequently, this research is focused on the thermal and chemical characterization of five different avocado seed oils depending on the maturity stage of the seed: 100% unripe, 25% mature-75% unripe, 50% mature-50% unripe, 75% mature-25% unripe, and 100% mature. The characterization was performed by differential scanning calorimetry, Fourier transform infrared spectroscopy, and thermogravimetric analysis. The best oil for natural environments corresponded to 100% matured seed with an enthalpy of fusion of 52.93 J·g−1, and a degradation temperature between 241–545 °C. In addition, the FTIR analysis shows that unripe seed oil seems to contain more lipids than a mature one. Furthermore, a simulation with an isothermal box was conducted with the characterized oil with an initial temperature of −14 °C for the isothermal box, −27 °C for the PCM box, and an ambient temperature of 25 °C. The results show that without the PCM the temperature can reach −8 °C and with it is −12 °C after 7 h, proving its application as a cold thermal energy system.

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