scholarly journals AMiGA: Software for Automated Analysis of Microbial Growth Assays

mSystems ◽  
2021 ◽  
Author(s):  
Firas S. Midani ◽  
James Collins ◽  
Robert A. Britton
Keyword(s):  
Microbial Growth ◽  
Growth Dynamics ◽  
Automated Analysis ◽  
Current Understanding ◽  
Microbial Populations ◽  
Simple Method ◽  
Microbial Physiology ◽  
Over Time

Our current understanding of microbial physiology relies on the simple method of measuring microbial populations’ sizes over time and under different conditions. Many advances have increased the throughput of those assays and enabled the study of nonlab-adapted microbes under diverse conditions that widely affect their growth dynamics.

scholarly journals AMiGA: software for automated Analysis of Microbial Growth Assays

2020 ◽  
Author(s):  
Firas S. Midani ◽  
James Collins ◽  
Robert A. Britton
Keyword(s):  
Microbial Growth ◽  
Growth Parameters ◽  
Growth Curves ◽  
Growth Dynamics ◽  
Automated Analysis ◽  
Growth Conditions ◽  
Differential Growth ◽  
Experimental Conditions ◽  
Simple Method ◽  
Organization Analysis

ABSTRACTThe analysis of microbial growth is one of the central methods in the field of microbiology. Microbial growth dynamics can be characterized by growth parameters including carrying capacity, exponential growth rate, and growth lag. However, growth assays with clinical isolates, fastidious organisms, or microbes under stress often produce atypical growth shapes that do not follow the classical microbial growth pattern. Here, we introduce the Analysis of Microbial Growth Assays (AMiGA) software which streamlines the analysis of growth curves without any assumptions about their shapes. AMiGA can pool replicates of growth curves and infer summary statistics for biologically meaningful growth parameters. In addition, AMiGA can quantify death phases and characterize diauxic shifts. It can also statistically test for differential growth under distinct experimental conditions. Altogether, AMiGA streamlines the organization, analysis, and visualization of microbial growth assays.IMPORTANCEOur current understanding of microbial physiology relies on the simple method of measuring microbial populations’ size over time and under different conditions. Many advances have increased the throughput of those assays and enabled the study of non-lab adapted microbes under diverse conditions that widely affect their growth dynamics. Our software provides an all-in-one tool for estimating the growth parameters of microbial cultures and testing for differential growth in a high-throughput and user-friendly fashion without any underlying assumptions about how microbes respond to their growth conditions.

scholarly journals Enhancement in physicochemical parameters and microbial populations of mushrooms as influenced by nano-coating treatments

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Rokayya Sami ◽  
Abeer Elhakem ◽  
Amina Almushhin ◽  
Mona Alharbi ◽  
Manal Almatrafi ◽  
...  
Keyword(s):  
Physicochemical Parameters ◽  
Microbial Growth ◽  
Research Work ◽  
Microbial Populations ◽  
Coating Film ◽  
Epidermal Structure ◽  
Nano Coating ◽  
Soluble Solid ◽  
Button Mushrooms ◽  
White Button Mushrooms

AbstractWhite button mushrooms are greatly high perishable and can deteriorate within a few days after harvesting due to physicomechanical damage, respiration, microbial growth of the delicate epidermal structure. For that reason, the present research work was applied to evaluate the effect of chitosan combination with nano-coating treatments on physicochemical parameters and microbial populations on button mushrooms at chilling storage. Nano coating with the addition of nisin 1% (CHSSN/M) established the minimum value for weight loss 12.18%, maintained firmness 11.55 N, and color index profile. Moreover, O2% rate of (CHSSN/M) mushrooms was the lowest at 1.78%; while the highest rate was reported for CO2 24.88% compared to the untreated samples (Control/M) on day 12. Both pH and total soluble solid concentrations increased during storage. Results reported that the (CHSS/M) mushroom significantly (P < 0.05) reduced polyphenol oxidase activity (24.31 U mg−1 Protein) compared with (Control/M) mushrooms that increased faster than the treated samples. (CHSSN/M) treatment was the most efficient in the reduction of yeast and mold, aerobic plate microorganisms (5.27–5.10 log CFU/g), respectively. The results established that nano-coating film might delay the aging degree and accompany by marked prolongation of postharvest mushroom freshness.

scholarly journals Automated analysis of filopodial length and spatially resolved protein concentration via adaptive shape tracking

2016 ◽  
Vol 27 (22) ◽  
pp. 3616-3626 ◽  
Author(s):  
Tanumoy Saha ◽  
Isabel Rathmann ◽  
Abhiyan Viplav ◽  
Sadhana Panzade ◽  
Isabell Begemann ◽  
...  
Keyword(s):  
Protein Concentration ◽  
Growth Dynamics ◽  
Automated Analysis ◽  
Cell Types ◽  
Control Mechanisms ◽  
Spatially Resolved ◽  
Novel Approach ◽  
Associated Proteins

Filopodia are dynamic, actin-rich structures that transiently form on a variety of cell types. To understand the underlying control mechanisms requires precise monitoring of localization and concentration of individual regulatory and structural proteins as filopodia elongate and subsequently retract. Although several methods exist that analyze changes in filopodial shape, a software solution to reliably correlate growth dynamics with spatially resolved protein concentration along the filopodium independent of bending, lateral shift, or tilting is missing. Here we introduce a novel approach based on the convex-hull algorithm for parallel analysis of growth dynamics and relative spatiotemporal protein concentration along flexible filopodial protrusions. Detailed in silico tests using various geometries confirm that our technique accurately tracks growth dynamics and relative protein concentration along the filopodial length for a broad range of signal distributions. To validate our technique in living cells, we measure filopodial dynamics and quantify spatiotemporal localization of filopodia-associated proteins during the filopodial extension–retraction cycle in a variety of cell types in vitro and in vivo. Together these results show that the technique is suitable for simultaneous analysis of growth dynamics and spatiotemporal protein enrichment along filopodia. To allow readily application by other laboratories, we share source code and instructions for software handling.

scholarly journals Competitive exclusion and metabolic dependency among microorganisms structure the cellulose economy of agricultural soil

2020 ◽  
Author(s):  
Roland C Wilhelm ◽  
Charles Pepe-Ranney ◽  
Pamela Weisenhorn ◽  
Mary Lipton ◽  
Daniel H. Buckley
Keyword(s):  
Microbial Growth ◽  
Competitive Exclusion ◽  
Antibiotic Production ◽  
Growth Dynamics ◽  
Soil Disturbance ◽  
Gliding Motility ◽  
Cellulolytic Microorganisms ◽  
Trade Offs ◽  
Self Sufficiency ◽  
Attachment Structures

Abstract Many cellulolytic microorganisms degrade cellulose through extracellular processes that yield free intermediates which promote interactions with non-cellulolytic organisms. We hypothesize that these interactions determine the ecological and physiological traits that govern the fate of cellulosic carbon (C) in soil. We evaluated the genomic potential of soil microorganisms that access C from 13 C-labeled cellulose. We used metagenomic-SIP and metaproteomics to evaluate whether cellulolytic and non-cellulolytic microbes that access 13 C from cellulose encode traits indicative of metabolic dependency or competitive exclusion. The most highly 13 C-enriched taxa were cellulolytic Cellvibrio ( Gammaproteobacteria ) and Chaetomium ( Ascomycota ), which exhibited a strategy of self-sufficiency (prototrophy), rapid growth, and competitive exclusion via antibiotic production. These ruderal taxa were common indicators of soil disturbance in agroecosystems, such as tillage and fertilization. Auxotrophy was more prevalent in cellulolytic Actinobacteria than in cellulolytic Proteobacteria , demonstrating differences in dependency among cellulose degraders. Non-cellulolytic taxa that accessed 13 C from cellulose ( Planctomycetales , Verrucomicrobia and Vampirovibrionales ) were highly dependent, as indicated by patterns of auxotrophy and 13 C-labeling (i.e. partial labelling or labeling at later-stages). Major 13 C-labeled cellulolytic microbes ( e.g. Sorangium, Actinomycetales, Rhizobiales and Caulobacteraceae ) possessed adaptations for surface colonization ( e.g. gliding motility, hyphae, attachment structures) signifying the importance of surface ecology in decomposition. These results suggest that access to cellulose was accompanied by ecological trade-offs characterized by differing degrees of metabolic dependency and competitive exclusion. These trade-offs likely influence microbial growth dynamics on particulate organic carbon and reveal that the fate of carbon is governed by a complex economy within the microbial community.

scholarly journals Effects of Replacing Extruded Maize by Dried Citrus Pulp in a Mixed Diet on Ruminal Fermentation, Methane Production, and Microbial Populations in Rusitec Fermenters

Animals ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1316
Author(s):  
Jairo García-Rodríguez ◽  
Cristina Saro ◽  
Iván Mateos ◽  
Jesús S. González ◽  
María Dolores Carro ◽  
...  
Keyword(s):  
Methane Production ◽  
Microbial Growth ◽  
Microbial Populations ◽  
Mixed Diet ◽  
Ruminal Fermentation ◽  
Citrus Industry ◽  
Ph Values ◽  
Citrus Pulp ◽  
Liquid Phases ◽  
Fermentation Parameters

Citrus pulp is a highly abundant by-product of the citrus industry. The aim of this study was to assess the effects of replacing extruded maize (EM; 20% of total diet) by dried citrus pulp (DCP; 20%) in a mixed diet on rumen fermentation and microbial populations in Rusitec fermenters. The two diets contained 50% alfalfa hay and 50% concentrate, and the same protein level. Four Rusitec fermenters were used in a cross-over design with two 13-d incubation runs. After 7-d of diet adaptation, diet disappearance, fermentation parameters, microbial growth, and microbial populations were assessed. Fermenters receiving the DCP showed greater pH values and fiber disappearance (p < 0.001) and lower methane production (p = 0.03) than those fed EM. Replacing EM by DCP caused an increase in the proportions of propionate and butyrate (p < 0.001) and a decrease in acetate (p = 0.04). Microbial growth, bacterial diversity, and the quantity of bacteria and protozoa DNA were not affected by the diet, but the relative abundances of fungi and archaea were greater (p < 0.03) in solid and liquid phases of DCP fermenters, respectively. Results indicate that DCP can substitute EM, promoting a more efficient ruminal fermentation.

scholarly journals Succession of microbial populations and nitrogen-fixation associated with the biodegradation of sediment-oil-agglomerates buried in a Florida sandy beach

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Boryoung Shin ◽  
Ioana Bociu ◽  
Max Kolton ◽  
Markus Huettel ◽  
Joel E. Kostka
Keyword(s):  
Nitrogen Fixation ◽  
Petroleum Hydrocarbons ◽  
Microbial Growth ◽  
Sandy Beach ◽  
Sandy Beaches ◽  
Beach Sand ◽  
Microbial Populations ◽  
In Situ Experiment ◽  
Potential Threat ◽  
Nitrogenase Genes

AbstractThe Deepwater Horizon (DWH) oil spill contaminated coastlines from Louisiana to Florida, burying oil up to 70 cm depth in sandy beaches, posing a potential threat to environmental and human health. The dry and nutrient-poor beach sand presents a taxing environment for microbial growth, raising the question how the biodegradation of the buried oil would proceed. Here we report the results of an in-situ experiment that (i) characterized the dominant microbial communities contained in sediment oil agglomerates (SOAs) of DWH oil buried in a North Florida sandy beach, (ii) elucidated the long-term succession of the microbial populations that developed in the SOAs, and (iii) revealed the coupling of SOA degradation to nitrogen fixation. Orders of magnitude higher bacterial abundances in SOAs compared to surrounding sands distinguished SOAs as hotspots of microbial growth. Blooms of bacterial taxa with a demonstrated potential for hydrocarbon degradation (Gammaproteobacteria, Alphaproteobacteria, Actinobacteria) developed in the SOAs, initiating a succession of microbial populations that mirrored the evolution of the petroleum hydrocarbons. Growth of nitrogen-fixing prokaryotes or diazotrophs (Rhizobiales and Frankiales), reflected in increased abundances of nitrogenase genes (nifH), catalyzed biodegradation of the nitrogen-poor petroleum hydrocarbons, emphasizing nitrogen fixation as a central mechanism facilitating the recovery of sandy beaches after oil contamination.

PREDOMINANT MICROORGANISMS ON RAW PLANT FOODS1,2

1970 ◽  
Vol 33 (11) ◽  
pp. 500-505 ◽  
Author(s):  
D. F. Splittstoesser
Keyword(s):  
Microbial Growth ◽  
Microbial Populations ◽  
Green Beans ◽  
Plant Foods ◽  
Microbial Counts ◽  
Equipment Contamination ◽  
Growth History

Considerable variation was observed in the microbial populations present on raw plant foods. Equipment contamination and microbial growth on the product following harvest often were responsible for high microbial counts. Because of these factors, vegetables protected by a pod or husk frequently were more heavily contaminated than those exposed to soil and air throughout their growth history. Similar types of microorganisms were isolated from raw and post-blanch samples of peas and green beans. The samples recontaminated after the blanch generally contained a higher proportion of catalase-negative cocci. Some of the properties of the more numerous groups are presented. Many of the isolates were sufficiently different from “type” cultures that they could not be readily placed into described species.

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