scholarly journals Bioanalytical insight into the life of microbial populations: a chemical monitoring of ureolytic bacteria growth

2021 ◽  
pp. 109899
Author(s):  
Justyna Bzura ◽  
Dorota Korsak ◽  
Robert Koncki
Keyword(s):  
Microbial Populations ◽  
Chemical Monitoring ◽  
Bacteria Growth ◽  
Insight Into ◽  
Ureolytic Bacteria

scholarly journals Compositional zero-inflated network estimation for microbiome data

2020 ◽  
Vol 21 (S21) ◽  
Author(s):  
Min Jin Ha ◽  
Junghi Kim ◽  
Jessica Galloway-Peña ◽  
Kim-Anh Do ◽  
Christine B. Peterson
Keyword(s):  
Oral Microbiome ◽  
Microbial Populations ◽  
High Throughput Data ◽  
Ecological Relationships ◽  
Network Estimation ◽  
Microbiome Data ◽  
Sparse Set ◽  
Insight Into ◽  
Continuous Representations ◽  
Critical Aspects

Abstract Background The estimation of microbial networks can provide important insight into the ecological relationships among the organisms that comprise the microbiome. However, there are a number of critical statistical challenges in the inference of such networks from high-throughput data. Since the abundances in each sample are constrained to have a fixed sum and there is incomplete overlap in microbial populations across subjects, the data are both compositional and zero-inflated. Results We propose the COmpositional Zero-Inflated Network Estimation (COZINE) method for inference of microbial networks which addresses these critical aspects of the data while maintaining computational scalability. COZINE relies on the multivariate Hurdle model to infer a sparse set of conditional dependencies which reflect not only relationships among the continuous values, but also among binary indicators of presence or absence and between the binary and continuous representations of the data. Our simulation results show that the proposed method is better able to capture various types of microbial relationships than existing approaches. We demonstrate the utility of the method with an application to understanding the oral microbiome network in a cohort of leukemic patients. Conclusions Our proposed method addresses important challenges in microbiome network estimation, and can be effectively applied to discover various types of dependence relationships in microbial communities. The procedure we have developed, which we refer to as COZINE, is available online at https://github.com/MinJinHa/COZINE.

scholarly journals Microbial Communities in the Fynbos Region of South Africa: What Happens during Woody Alien Plant Invasions

Diversity ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 254
Author(s):  
Karin Jacobs ◽  
Tersia Conradie ◽  
Shayne Jacobs
Keyword(s):  
Current Knowledge ◽  
Plant Invasions ◽  
Cape Floristic Region ◽  
Alien Plants ◽  
Microbial Populations ◽  
Invasive Alien Plants ◽  
Alien Plant ◽  
Lack Of Information ◽  
The Common ◽  
Insight Into

The Cape Floristic Region (CFR) is globally known for its plant biodiversity, and its flora is commonly referred to as fynbos. At the same time, this area is under severe pressure from urbanization, agricultural expansion and the threat of invasive alien plants. Acacia, Eucalyptus and Pinus are the common invasive alien plants found across the biome and considerable time, effort and resources are put into the removal of invasive alien plants and the rehabilitation of native vegetation. Several studies have shown that invasion not only affects the composition of plant species, but also has a profound effect on the soil chemistry and microbial populations. Over the last few years, a number of studies have shown that the microbial populations of the CFR are unique to the area, and harbour many endemic species. The extent of the role they play in the invasion process is, however, still unclear. This review aims to provide an insight into the current knowledge on the different microbial populations from this system, and speculate what their role might be during invasion. More importantly, it places a spotlight on the lack of information about this process.

scholarly journals The pelvic flexure separates distinct microbial communities in the equine hindgut

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kailee J. Reed ◽  
Isabelle G. Z. Kunz ◽  
Jessica A. Scare ◽  
Martin K. Nielsen ◽  
Philip J. Turk ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Fecal Microbiota ◽  
Microbial Populations ◽  
Digestive Physiology ◽  
Distinct Population ◽  
Species Analysis ◽  
Gut Homeostasis ◽  
Population Structures ◽  
Microbial Dna ◽  
Insight Into

AbstractAs hindgut fermenters, horses are especially dependent on the microbiota residing in their cecum and large intestines. Interactions between these microbial populations and the horse are critical for maintaining gut homeostasis, which supports proper digestion. The current project was motivated to determine if any features of the fecal microbiota are informative of the microbial communities from the cecum, ventral colon, or dorsal colon. Digesta from the cecum, ventral colon, dorsal colon and feces were collected from 6 yearling miniature horses. Microbial DNA was isolated and the microbiota from each sample was characterized by profiling the V4 region of the 16S rRNA. Principal coordinate analysis of the beta diversity results revealed significant (p = 0.0001; F = 5.2393) similarities between the microbial populations from cecal and ventral colon and the dorsal colon and fecal samples, however, there was little overlap between the proximal and distal ends of the hindgut. These distinct population structures observed in our results coincide with the pelvic flexure, which itself separates intestinal compartments with distinct roles in digestive physiology. An indicator species analysis confirmed the population differences, supported by the identification of several microbial families characteristic of the compartments upstream of the pelvic flexure that were not represented following it. Our data suggest that the fecal microbiota is not informative of the proximal hindgut but can provide insight into communities of the distal compartments. Further, our results suggest that the pelvic flexure might be an important anatomical landmark relative to the microbial communities in the equine large intestine.

scholarly journals ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data

2019 ◽  
Author(s):  
Silas Kieser ◽  
Joseph Brown ◽  
Evgeny M. Zdobnov ◽  
Mirko Trajkovski ◽  
Lee Ann McCue
Keyword(s):  
Data Processing ◽  
Sequence Data ◽  
Microbial Populations ◽  
Valuable Insight ◽  
Genome Databases ◽  
Abundance Estimates ◽  
And Function ◽  
User Friendly ◽  
Insight Into ◽  
Metagenome Sequence

AbstractBackgroundMetagenomics and metatranscriptomics studies provide valuable insight into the composition and function of microbial populations from diverse environments, however the data processing pipelines that rely on mapping reads to gene catalogs or genome databases for cultured strains yield results that underrepresent the genes and functional potential of uncultured microbes. Recent improvements in sequence assembly methods have eased the reliance on genome databases, thereby allowing the recovery of genomes from uncultured microbes. However, configuring these tools, linking them with advanced binning and annotation tools, and maintaining provenance of the processing continues to be challenging for researchers.ResultsHere we present ATLAS, a software package for customizable data processing from raw sequence reads to functional and taxonomic annotations using state-of-the-art tools to assemble, annotate, quantify, and bin metagenome and metatranscriptome data. Genome-centric resolution and abundance estimates are provided for each sample in a dataset. ATLAS is written in Python and the workflow implemented in Snakemake; it operates in a Linux environment, and is compatible with Python 3.5+ and Anaconda 3+ versions. The source code for ATLAS is freely available, distributed under a BSD-3 license.ConclusionATLAS provides a user-friendly, modular and customizable Snakemake workflow for metagenome and metatranscriptome data processing; it is easily installable with conda and maintained as open-source on GitHub at https://github.com/metagenome-atlas/atlas.

scholarly journals Microbial community transcriptional networks are conserved in three domains at ocean basin scales

2015 ◽  
Vol 112 (17) ◽  
pp. 5443-5448 ◽  
Author(s):  
Frank O. Aylward ◽  
John M. Eppley ◽  
Jason M. Smith ◽  
Francisco P. Chavez ◽  
Christopher A. Scholin ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Biotic Interactions ◽  
Ocean Basin ◽  
Microbial Populations ◽  
Transcriptional Networks ◽  
Biological Interactions ◽  
North Pacific Subtropical Gyre ◽  
Diel Cycles ◽  
Genome Wide ◽  
Insight Into

Planktonic microbial communities in the ocean are typically dominated by several cosmopolitan clades ofBacteria,Archaea, andEukaryacharacterized by their ribosomal RNA gene phylogenies and genomic features. Although the environments these communities inhabit range from coastal to open ocean waters, how the biological dynamics vary between such disparate habitats is not well known. To gain insight into the differential activities of microbial populations inhabiting different oceanic provinces we compared the daily metatranscriptome profiles of related microbial populations inhabiting surface waters of both a coastal California upwelling region (CC) as well as the oligotrophic North Pacific Subtropical Gyre (NPSG). Transcriptional networks revealed that the dominant photoautotrophic microbes in each environment (Ostreococcusin CC,Prochlorococcusin NPSG) were central determinants of overall community transcriptome dynamics. Furthermore, heterotrophic bacterial clades common to both ecosystems (SAR11, SAR116, SAR86, SAR406, andRoseobacter) displayed conserved, genome-wide inter- and intrataxon transcriptional patterns and diel cycles. Populations of SAR11 and SAR86 clades in particular exhibited tightly coordinated transcriptional patterns in both coastal and pelagic ecosystems, suggesting that specific biological interactions between these groups are widespread in nature. Our results identify common diurnally oscillating behaviors among diverse planktonic microbial species regardless of habitat, suggesting that highly conserved temporally phased biotic interactions are ubiquitous among planktonic microbial communities worldwide.

Calibration problems in hydrogen luminosities

1966 ◽  
Vol 24 ◽  
pp. 322-330
Author(s):  
A. Beer
Keyword(s):  
Galactic Structure ◽  
B Stars ◽  
Insight Into

The investigations which I should like to summarize in this paper concern recent photo-electric luminosity determinations of O and B stars. Their final aim has been the derivation of new stellar distances, and some insight into certain patterns of galactic structure.

Stochasting modeling of planetary ring systems

1984 ◽  
Vol 75 ◽  
pp. 461-469 ◽  
Author(s):  
Robert W. Hart
Keyword(s):  
Maximum Entropy ◽  
Ring System ◽  
The Sun ◽  
Ultimate State ◽  
Interparticle Interactions ◽  
Ring Systems ◽  
First Order ◽  
Planetary Ring ◽  
Insight Into

ABSTRACTThis paper models maximum entropy configurations of idealized gravitational ring systems. Such configurations are of interest because systems generally evolve toward an ultimate state of maximum randomness. For simplicity, attention is confined to ultimate states for which interparticle interactions are no longer of first order importance. The planets, in their orbits about the sun, are one example of such a ring system. The extent to which the present approximation yields insight into ring systems such as Saturn's is explored briefly.

Skeletal elements of crinoid echinoderms: High-resolution structural and microanalytical results

1983 ◽  
Vol 41 ◽  
pp. 194-195
Author(s):  
D. F. Blake ◽  
L. F. Allard ◽  
D. R. Peacor
Keyword(s):  
High Resolution ◽  
Marine Invertebrates ◽  
Sea Urchins ◽  
Structural Features ◽  
Sea Stars ◽  
High Resolution Tem ◽  
Relationship Of ◽  
The Relationship ◽  
Insight Into

Echinodermata is a phylum of marine invertebrates which has been extant since Cambrian time (c.a. 500 m.y. before the present). Modern examples of echinoderms include sea urchins, sea stars, and sea lilies (crinoids). The endoskeletons of echinoderms are composed of plates or ossicles (Fig. 1) which are with few exceptions, porous, single crystals of high-magnesian calcite. Despite their single crystal nature, fracture surfaces do not exhibit the near-perfect {10.4} cleavage characteristic of inorganic calcite. This paradoxical mix of biogenic and inorganic features has prompted much recent work on echinoderm skeletal crystallography. Furthermore, fossil echinoderm hard parts comprise a volumetrically significant portion of some marine limestones sequences. The ultrastructural and microchemical characterization of modern skeletal material should lend insight into: 1). The nature of the biogenic processes involved, for example, the relationship of Mg heterogeneity to morphological and structural features in modern echinoderm material, and 2). The nature of the diagenetic changes undergone by their ancient, fossilized counterparts. In this study, high resolution TEM (HRTEM), high voltage TEM (HVTEM), and STEM microanalysis are used to characterize tha ultrastructural and microchemical composition of skeletal elements of the modern crinoid Neocrinus blakei.

Structure and function of neural networks in the retina

1988 ◽  
Vol 46 ◽  
pp. 26-27
Author(s):  
Peter Sterling
Keyword(s):  
Ganglion Cells ◽  
Three Dimensional ◽  
Structure And Function ◽  
Synaptic Connections ◽  
Visual Axis ◽  
One Dimensional ◽  
Cat Retina ◽  
Ultrathin Sections ◽  
And Function ◽  
Insight Into

The synaptic connections in cat retina that link photoreceptors to ganglion cells have been analyzed quantitatively. Our approach has been to prepare serial, ultrathin sections and photograph en montage at low magnification (˜2000X) in the electron microscope. Six series, 100-300 sections long, have been prepared over the last decade. They derive from different cats but always from the same region of retina, about one degree from the center of the visual axis. The material has been analyzed by reconstructing adjacent neurons in each array and then identifying systematically the synaptic connections between arrays. Most reconstructions were done manually by tracing the outlines of processes in successive sections onto acetate sheets aligned on a cartoonist's jig. The tracings were then digitized, stacked by computer, and printed with the hidden lines removed. The results have provided rather than the usual one-dimensional account of pathways, a three-dimensional account of circuits. From this has emerged insight into the functional architecture.

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