scholarly journals Linking comparative genomics and environmental distribution patterns of microbial populations through metagenomics

2016 ◽  
Author(s):  
Tom O. Delmont ◽  
A. Murat Eren
Keyword(s):  
Comparative Genomics ◽  
Distribution Patterns ◽  
Deepwater Horizon ◽  
Microbial Populations ◽  
Environmental Distribution ◽  
Bacterial Populations ◽  
Rare Biosphere ◽  
Microbial Response ◽  
New Findings ◽  
Entire Gene

AbstractCombining well-established practices from comparative genomics and the emerging opportunities from assembly-based metagenomics can enhance the utility of increasing number of metagenome-assembled genomes (MAGs). Here we used protein clustering to characterize 48 MAGs and 10 cultivars based on their entire gene content, and linked this information to their environmental distribution patterns to better understand the microbial response to the 2010 Deepwater Horizon oil spill in the Gulf of Mexico coastline. Our results suggest that while most oil-associated bacterial populations originated from the ocean, a few actually emerged from the sand rare biosphere. These new findings suggest that there are considerable benefits to employ approaches from comparative genomics to study the whole content of newly identified genomes, and the investigation of emerging patterns in the environmental context can augment the efficacy of assembly-based metagenomic surveys.

scholarly journals On the Variability of Microbial Populations and Bacterial Metabolites within the Canine Stool. An in-Depth Analysis

Animals ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 225
Author(s):  
Carlo Pinna ◽  
Carla Giuditta Vecchiato ◽  
Costanza Delsante ◽  
Monica Grandi ◽  
Giacomo Biagi
Keyword(s):  
Distribution Patterns ◽  
Short Chain Fatty Acids ◽  
Microbial Populations ◽  
Contradictory Result ◽  
Bacterial Populations ◽  
Bacterial Metabolites ◽  
Faecal Samples ◽  
Depth Analysis ◽  
Enterococcus Spp ◽  
Before And After

Canine faecal microbial populations and metabolome are being increasingly studied to understand the interplay between host and gut microbiome. However, the distribution of bacterial taxa and microbial metabolites throughout the canine stool is understudied and currently no guidelines for the collection, storage and preparation of canine faecal samples have been proposed. Here, we assessed the effects that different sampling points have on the abundance of selected microbial populations and bacterial metabolites within the canine stool. Whole fresh faecal samples were obtained from five healthy adult dogs. Stool subsamples were collected from the surface to the inner part and from three equally sized areas (cranial, central, caudal) along the length axis of the stool log. All samples were finally homogenised and compared before and after homogenisation. Firmicutes, Bacteroidetes, Clostridium cluster I, Lactobacillus spp., Bifidobacterium spp. and Enterococcus spp. populations were analysed, as well as pH, ammonia and short-chain fatty acids (SCFA) concentrations. Compared to the surface of the stool, inner subsamples resulted in greater concentrations of SCFA and ammonia, and lower pH values. qPCR assay of microbial taxa did not show any differences between subsamples. Homogenisation of faeces does not affect the variability of microbial and metabolome data. Although the distribution patterns of bacterial populations and metabolites are still unclear, we found that stool subsampling yielded contradictory result and biases that can affect the final outcome when investigating the canine microbiome. Complete homogenisation of the whole stool is therefore recommended.

scholarly journals Temperature Sensitivity and Composition of Nitrate-Reducing Microbiomes from a Full-Scale Woodchip Bioreactor Treating Agricultural Drainage Water

2021 ◽  
Vol 9 (6) ◽  
pp. 1331
Author(s):  
Arnaud Jéglot ◽  
Sebastian Reinhold Sørensen ◽  
Kirk M. Schnorr ◽  
Finn Plauborg ◽  
Lars Elsgaard
Keyword(s):  
Temperature Response ◽  
Microbial Transformation ◽  
Drainage Water ◽  
Microbial Populations ◽  
Agricultural Drainage ◽  
Bacterial Populations ◽  
Cold Temperatures ◽  
Cold Adapted ◽  
Agricultural Drainage Water ◽  
Temperature Responses

Denitrifying woodchip bioreactors (WBR), which aim to reduce nitrate (NO3−) pollution from agricultural drainage water, are less efficient when cold temperatures slow down the microbial transformation processes. Conducting bioaugmentation could potentially increase the NO3− removal efficiency during these specific periods. First, it is necessary to investigate denitrifying microbial populations in these facilities and understand their temperature responses. We hypothesized that seasonal changes and subsequent adaptations of microbial populations would allow for enrichment of cold-adapted denitrifying bacterial populations with potential use for bioaugmentation. Woodchip material was sampled from an operating WBR during spring, fall, and winter and used for enrichments of denitrifiers that were characterized by studies of metagenomics and temperature dependence of NO3− depletion. The successful enrichment of psychrotolerant denitrifiers was supported by the differences in temperature response, with the apparent domination of the phylum Proteobacteria and the genus Pseudomonas. The enrichments were found to have different microbiomes’ composition and they mainly differed with native woodchip microbiomes by a lower abundance of the genus Flavobacterium. Overall, the performance and composition of the enriched denitrifying population from the WBR microbiome indicated a potential for efficient NO3− removal at cold temperatures that could be stimulated by the addition of selected cold-adapted denitrifying bacteria.

Effects of potassium azide on soil microbial populations and soil enzymatic activities

1975 ◽  
Vol 21 (4) ◽  
pp. 565-570 ◽  
Author(s):  
W. D. Kelley ◽  
R. Rodriguez-Kabana
Keyword(s):  
Soil Enzyme ◽  
Soil Microflora ◽  
Microbial Populations ◽  
Bacterial Populations ◽  
Soil Microbial ◽  
Fungal Populations ◽  
Potassium Azide ◽  
Time Changes ◽  
Bacteria And Fungi ◽  
Microbial Numbers

Preplant applications of potassium azide (KN3) to pine nursery beds were evaluated for effect on the soil microflora and on soil enzyme activity where either plastic-sealing or water-sealing techniques were used. Two weeks after incorporation of azide (0–224 kg/ha), soil samplings revealed reduced populations of bacteria and fungi and a corresponding decline in invertase and amylase activities. These effects were proportionate to the amount of azide used and were more pronounced in plastic-sealed plots. Phosphatase activity was little affected. Five weeks after azide application, bacterial populations were higher in treated plots than in controls. Greater numbers of bacteria were recorded from plastic-sealed plots and highest populations coincided with plots receiving the highest rates of azide, regardless of the sealing technique. Fungal populations at this sampling were generally less in treated plots than in the controls, but were higher under plastic seal. At this time, changes in invertase and amylase activities did not correspond to increased microbial numbers. Sixteen weeks after applications of KN3, bacterial populations in treated plots did not differ significantly from controls, but remained higher in plastic-sealed than water-sealed plots. Fungal populations under plastic seal had changed little and remained significantly lower in treated water-sealed plots than in controls. The earlier recorded reduction in invertase and amylase activities was still evident at the final sampling.

scholarly journals Fitness Trade-Offs in blaTEM Evolution

2008 ◽  
Vol 52 (7) ◽  
pp. 2340-2345 ◽  
Author(s):  
Joanna E. Mroczkowska ◽  
Miriam Barlow
Keyword(s):  
Microbial Populations ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Bacterial Populations ◽  
Real Time Quantitative Pcr ◽  
Fitness Effects ◽  
Fitness Advantage ◽  
Extended Spectrum ◽  
Trade Offs ◽  
Pcr Method

ABSTRACT bla TEM-1 expression results in penicillin resistance, whereas expression of many bla TEM-1 descendants, called extended-spectrum β-lactamases (ESBLs), results simultaneously in resistance to penicillins and extended-spectrum cephalosporins. Despite the expanded resistance phenotypes conferred by many ESBLs, bla TEM-1 is still the most abundant bla TEM allele in many microbial populations. This study examines the fitness effects of the two amino acid substitutions, R164S and E240K, that have occurred repeatedly among ESBL bla TEM-1 descendants. Using a single-nucleotide polymorphism-specific real-time quantitative PCR method, we analyzed the fitness of strains expressing bla TEM-1, bla TEM-10, and bla TEM-12. Our results show that bacteria expressing the ancestral bla TEM-1 allele have a fitness advantage over those expressing either bla TEM-10 or bla TEM-12 when exposed to ampicillin. This observation, combined with the fact that penicillins are the most prevalent antimicrobials prescribed worldwide, may explain why bla TEM-1 has persisted as the most frequently encountered bla TEM allele in bacterial populations.

Microbiological Status of Fresh Beef Cuts

2006 ◽  
Vol 69 (6) ◽  
pp. 1456-1459 ◽  
Author(s):  
J. D. STOPFORTH ◽  
M. LOPES ◽  
J. E. SHULTZ ◽  
R. R. MIKSCH ◽  
M. SAMADPOUR
Keyword(s):  
Total Coliform ◽  
Incidence Rates ◽  
Microbial Populations ◽  
Plate Count ◽  
Bacterial Populations ◽  
E Coli ◽  
Coliform Count ◽  
Processing Plants ◽  
Aerobic Plate Count ◽  
Whole Muscle

Fresh beef samples (n = 1,022) obtained from two processing plants in the Midwest (July to December 2003) were analyzed for levels of microbial populations (total aerobic plate count, total coliform count, and Escherichia coli count) and for the presence or absence of E. coli O157:H7 and Salmonella. A fresh beef cut sample was a 360-g composite of 6-g portions excised from the surface of 60 individual representative cuts in a production lot. Samples of fresh beef cuts yielded levels of 4.0 to 6.2, 1.1 to 1.8, and 0.8 to 1.0 log CFU/g for total aerobic plate count, total coliform count, and E. coli count, respectively. There did not appear to be substantial differences or obvious trends in bacterial populations on different cuts. These data may be useful in establishing a baseline or a benchmark of microbiological levels of contamination of beef cuts. Mean incidence rates of E. coli O157:H7 and Salmonella on raw beef cuts were 0.3 and 2.2%, respectively. Of the 1,022 samples analyzed, cuts testing positive for E. coli O157:H7 included top sirloin butt (0.9%) and butt, ball tip (2.1%) and for Salmonella included short loins (3.4%), strip loins (9.6%), rib eye roll (0.8%), shoulder clod (3.4%), and clod, top blade (1.8%). These data provide evidence of noticeable incidence of pathogens on whole muscle beef and raise the importance of such contamination on product that may be mechanically tenderized. Levels of total aerobic plate count, total coliform count, and E. coli count did not (P ≥ 0.05) appear to be associated with the presence of E. coli O157:H7 and Salmonella on fresh beef cuts. E. O157:H7 was exclusively isolated from cuts derived from the sirloin area of the carcass. Salmonella was exclusively isolated from cuts derived from the chuck, rib, and loin areas of the carcass. Results of this study suggest that contamination of beef cuts may be influenced by the region of the carcass from which they are derived.

scholarly journals Relative sorption coefficient: Key to tracing petroleum migration and other subsurface fluids

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
L. Zhang ◽  
Y. Wang ◽  
M.-W. Li ◽  
Q.-Z. Yin ◽  
W. Zhang
Keyword(s):  
Sedimentary Basins ◽  
Distribution Patterns ◽  
Polar Compounds ◽  
Source Rocks ◽  
Polar Molecules ◽  
Sorption Coefficient ◽  
Petroleum Migration ◽  
New Findings ◽  
Novel Concept ◽  
Incorrect Information

AbstractThe accumulation and spatial distribution of economically important petroleum in sedimentary basins are primarily controlled by its migration from source rocks through permeable carrier beds to reservoirs. Tracing petroleum migration entails the use of molecular indices established according to sorption capacities of polar molecules in migrating petroleum. However, little is known about molecular sorption capacities in natural migration systems, rendering these indices unreliable. Here, we present a new approach based on a novel concept of relative sorption coefficient for quantitatively assessing sorption capacities of polar molecules during natural petroleum migration. Using this approach, we discovered previously unrecognized “stripping” and “impeding” effects that significantly reduce the sorption capacities of polar compounds. These discoveries provide new insights into the behaviors of polar compounds and can easily explain why traditional molecular indices yield incorrect information about petroleum migration. In light of these new findings, we established new molecular indices for tracing petroleum migration. We demonstrate via case studies that the newly established indices, unlike traditional molecular indices, are reliable and effective in tracing petroleum migration. Our approach can be applied to diverse basins around the world to reveal distribution patterns of petroleum, which would decrease environmental risks of exploration by reducing unsuccessful wells.

scholarly journals Web-gLV: A Web Based Platform for Lotka-Volterra Based Modeling and Simulation of Microbial Populations

2019 ◽  
Vol 10 ◽  
Author(s):  
Bhusan K. Kuntal ◽  
Chetan Gadgil ◽  
Sharmila S. Mande
Keyword(s):  
Modeling And Simulation ◽  
Time Series Data ◽  
Microbial Populations ◽  
Series Data ◽  
Estimation Of Parameters ◽  
Valuable Contribution ◽  
Bacterial Populations ◽  
Web Based ◽  
Automatic Estimation ◽  
High Throughput Dna Sequencing

The affordability of high throughput DNA sequencing has allowed us to explore the dynamics of microbial populations in various ecosystems. Mathematical modeling and simulation of such microbiome time series data can help in getting better understanding of bacterial communities. In this paper, we present Web-gLV—a GUI based interactive platform for generalized Lotka-Volterra (gLV) based modeling and simulation of microbial populations. The tool can be used to generate the mathematical models with automatic estimation of parameters and use them to predict future trajectories using numerical simulations. We also demonstrate the utility of our tool on few publicly available datasets. The case studies demonstrate the ease with which the current tool can be used by biologists to model bacterial populations and simulate their dynamics to get biological insights. We expect Web-gLV to be a valuable contribution in the field of ecological modeling and metagenomic systems biology.

Bacterial Populations of Ground Beef, Textured Soy Protein and Ground Beef Extended With Soy Protein After 3 and 10 Days of Refrigerated Storage1,2

1978 ◽  
Vol 41 (8) ◽  
pp. 647-653 ◽  
Author(s):  
JAMES F. FOSTER ◽  
RICHARD C. HUNDERFUND ◽  
JAMES L. FOWLER ◽  
JOHN T. FRUIN ◽  
LINDA S. GUTHERTZ
Keyword(s):  
Soy Protein ◽  
Ground Beef ◽  
Microbial Populations ◽  
Plate Count ◽  
Most Probable Number ◽  
Bacterial Populations ◽  
Probable Number ◽  
Fecal Streptococcus ◽  
Large Numbers ◽  
Aerobic Plate Count

A survey of the microbial populations of 31 samples of ground beef (GB), textured soy protein (TSP), and ground beef extended with TSP (SGB) after 3 and 10 days of storage at 4 C was done. Analyses included aerobic plate count (APC), psychrotrophic plate count (PPC), coliform Most Probable Number (CMPN) and plate determinations (CPC), Escherichia coli MPN (EMPN) and plate determinations (EPC), Staphylococcus aureus MPN, and fecal streptococcus plate count. Statistical analyses of data from the enumeration procedures showed significant increases in the total microbial flora after 10 days of storage. PPCs were significantly higher than APCs. CMPNs were significantly higher than CPCs for GB and SGB. The EMPNs were significantly higher than EPCs in SGB only. These products contained a variety of microorganisms many in large numbers; however if properly handled and cooked before consumption, these products should present no public health problems.

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