Dietary pea fibre alters the microbial community and fermentation with increase in fibre degradation-associated bacterial groups in the colon of pigs

2017 ◽  
Vol 102 (1) ◽  
pp. e254-e261 ◽  
Author(s):  
Y. Luo ◽  
H. Chen ◽  
B. Yu ◽  
J. He ◽  
P. Zheng ◽  
...  
Keyword(s):  
Microbial Community ◽  
Fibre Degradation ◽  
Bacterial Groups

scholarly journals Development of microbial community in the course of composting of garden waste

2012 ◽  
Vol 60 (3) ◽  
pp. 225-232 ◽  
Author(s):  
Monika Vítězová ◽  
Pavel Mach ◽  
Tomáš Vítěz ◽  
Tomáš Lošák
Keyword(s):  
Microbial Community ◽  
Total Nitrogen ◽  
Municipal Waste ◽  
Total Carbon ◽  
Biochemical Tests ◽  
Carbon To Nitrogen Ratio ◽  
Nitrogen Ratio ◽  
Bacterial Groups ◽  
Garden Waste

Composting represents one of the technologies of processing of biodegradable municipal waste. Samples collected from composting plants were analyzed chemically, physically and microbiologically. The pH of bio waste samples increased from 6.5 to 8.6. The total carbon to nitrogen ratio in samples of bio waste decreased, in the course of composting, from 40:1 up to the value of 25:1 while the total nitrogen to phosphorus ratio decreased from 10:1 up to 8:1. Indicator groups of microorganisms were monitored in compost samples. Representatives of Enterobacter genus, namely E. cloacae and E. aerogenes were identified in the samples on the basis of biochemical tests. The bacterial groups needed for efficient composting, i.e. order Bacillales and Actinomycetales, were present in appreciable amounts.

scholarly journals A distinct and active bacterial community in cold oxygenated fluids circulating beneath the western flank of the Mid-Atlantic ridge

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Julie L. Meyer ◽  
Ulrike Jaekel ◽  
Benjamin J. Tully ◽  
Brian T. Glazer ◽  
C. Geoffrey Wheat ◽  
...  
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Elevated Temperatures ◽  
Geochemical Composition ◽  
Crustal Fluid ◽  
Functional Potential ◽  
Mid Atlantic Ridge ◽  
Bacterial Groups ◽  
Insight Into

Abstract The rock-hosted, oceanic crustal aquifer is one of the largest ecosystems on Earth, yet little is known about its indigenous microorganisms. Here we provide the first phylogenetic and functional description of an active microbial community residing in the cold oxic crustal aquifer. Using subseafloor observatories, we recovered crustal fluids and found that the geochemical composition is similar to bottom seawater, as are cell abundances. However, based on relative abundances and functional potential of key bacterial groups, the crustal fluid microbial community is heterogeneous and markedly distinct from seawater. Potential rates of autotrophy and heterotrophy in the crust exceeded those of seawater, especially at elevated temperatures (25 °C) and deeper in the crust. Together, these results reveal an active, distinct, and diverse bacterial community engaged in both heterotrophy and autotrophy in the oxygenated crustal aquifer, providing key insight into the role of microbial communities in the ubiquitous cold dark subseafloor biosphere.

scholarly journals Bacterial community analysis in the rice straw sample before and after composting by PCR-DGGE and cloning method

2020 ◽  
Vol 18 (1) ◽  
pp. 177-186
Author(s):  
Ngo Duc Duy ◽  
Nguyen Hoang Dung ◽  
Hoang Quoc Khanh
Keyword(s):  
Microbial Community ◽  
Rice Straw ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Bacillus Species ◽  
Study Results ◽  
Cloning Method ◽  
Before And After ◽  
Polymerase Chain ◽  
Bacterial Groups

Applicability of PCR-DGGE (Polymerase Chain Reaction-Denaturing Gel Gradient Eletrophoresis) technique to analyze microbial community is based on the V3 gene fragments in the rice straw sample (R) and after composting rice straw samples (Rn). Besides clonning method combined with analyzing Rn samples and comparing the results of microbial community analysis with PCR-DGGE method had the same reuslts is the main goal in this study. Results obtained from PCR-DGGE technique of R sample had 5 the V3 gene fragments (R1, R2, R3, R4 and R5) and Rn had 4 the V3 genes fragments (Rn1, Rn2, Rn3 and Rn4). Comparison of bacterial groups in R and Rn samples showed that bacteria in R samples including Agrobacterium, Clostridium, Bacteroidetes, Thermopolysporasa and Bacillus species, but in the Rn sample after incubation, the remaining bacterial results of 2 main species are Agrobacterium and Clostridium. Using Clonning method of Rn sample also gave 4 positions and gene fragment sizes corresponding to the positions of Rn1, Rn2, Rn3 and Rn4 from representatives of about 30 samples collected from the Clonning products. Based on the comparison of the similarity among the sequence of V3 gene fragments in PCR-DGGE and Clonning with reference to the data base in NCBI gene bank the results that Rn1 and Rn4 genes are similar to Agrobacterium species, about 96%, Rn2 and Rn3 are similar to Clostridium about 99%. In summary the results of microbial community analysis in the R sample show that the diversity of bacteria in the R sample is larger than in the Rn sample. Summarize the results of microbial community analysis in the R sample show the diversity of bacteria but less stable than the Rn sample. In addition, cloning and PCR-DGGE produced similar results on the sample Rn.

scholarly journals The amphibian microbiome exhibits poor resilience following pathogen-induced disturbance

2021 ◽  
Author(s):  
Andrea J. Jani ◽  
Jessie Bushell ◽  
Cédric G. Arisdakessian ◽  
Mahdi Belcaid ◽  
Daniel M. Boiano ◽  
...  
Keyword(s):  
Microbial Community ◽  
Batrachochytrium Dendrobatidis ◽  
Recovery Period ◽  
Stable State ◽  
Amphibian Skin ◽  
Unifrac Distance ◽  
Microbiome Composition ◽  
Relative Abundances ◽  
Community Variability ◽  
Bacterial Groups

AbstractInfectious pathogens can disrupt the microbiome in addition to directly affecting the host. Impacts of disease may be dependent on the ability of the microbiome to recover from such disturbance, yet remarkably little is known about microbiome recovery after disease, particularly in nonhuman animals. We assessed the resilience of the amphibian skin microbial community after disturbance by the pathogen, Batrachochytrium dendrobatidis (Bd). Skin microbial communities of laboratory-reared mountain yellow-legged frogs were tracked through three experimental phases: prior to Bd infection, after Bd infection (disturbance), and after clearing Bd infection (recovery period). Bd infection disturbed microbiome composition and altered the relative abundances of several dominant bacterial taxa. After Bd infection, frogs were treated with an antifungal drug that cleared Bd infection, but this did not lead to recovery of microbiome composition (measured as Unifrac distance) or relative abundances of dominant bacterial groups. These results indicate that Bd infection can lead to an alternate stable state in the microbiome of sensitive amphibians, or that microbiome recovery is extremely slow—in either case resilience is low. Furthermore, antifungal treatment and clearance of Bd infection had the additional effect of reducing microbial community variability, which we hypothesize results from similarity across frogs in the taxa that colonize community vacancies resulting from the removal of Bd. Our results indicate that the skin microbiota of mountain yellow-legged frogs has low resilience following Bd-induced disturbance and is further altered by the process of clearing Bd infection, which may have implications for the conservation of this endangered amphibian.

scholarly journals Characterization of the Cricket Hindgut Microbiota with Fluorescently Labeled rRNA-Targeted Oligonucleotide Probes

1998 ◽  
Vol 64 (2) ◽  
pp. 752-755 ◽  
Author(s):  
Jorge W. Santo Domingo ◽  
Michael G. Kaufman ◽  
Michael J. Klug ◽  
James M. Tiedje
Keyword(s):  
Microbial Community ◽  
Oligonucleotide Probes ◽  
Bacterial Groups

ABSTRACT Most cricket hindgut microorganisms (60 to 80%) were detected with a universal fluorescent rRNA-targeted probe and found to be eubacteria. Group-specific probes showed that the hindguts of five different cricket species harbor similar bacterial groups, although in different proportions, and that different diets shifted the structure of the hindgut microbial community. The Bacteroides-Prevotellaprobe, of the eight eubacterial probes tested, stained the largest percentage of cells in all crickets.

scholarly journals Combined Effects of Compost and Medicago Sativa in Recovery a PCB Contaminated Soil

Water ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 860 ◽  
Author(s):  
Martina Di Lenola ◽  
Anna Barra Caracciolo ◽  
Valeria Ancona ◽  
Vito Armando Laudicina ◽  
Gian Luigi Garbini ◽  
...  
Keyword(s):  
Microbial Community ◽  
Cell Viability ◽  
Medicago Sativa ◽  
Soil Samples ◽  
Combined Effects ◽  
Phylogenetic Characterization ◽  
Natural Microbial Community ◽  
Fixed Times ◽  
Bacterial Groups

The effectiveness of adding compost and the plant Medicago sativa in improving the quality of a soil historically contaminated by polychlorinated biphenyls (PCBs) was tested in greenhouse microcosms. Plant pots, containing soil samples from an area contaminated by PCBs, were treated with the compost and the plant, separately or together. Moreover, un-treated and un-planted microcosms were used as controls. At fixed times (1, 133 and 224 days), PCBs were analysed and the structure (cell abundance, phylogenetic characterization) and functioning (cell viability, dehydrogenase activity) of the natural microbial community were also measured. The results showed the effectiveness of the compost and plant in increasing the microbial activity, cell viability, and bacteria/fungi ratio, and in decreasing the amount of higher-chlorinated PCBs. Moreover, a higher number of α-Proteobacteria, one of the main bacterial groups involved in the degradation of PCBs, was found in the compost and plant co-presence.

scholarly journals Phycosphere Microbial Succession Patterns and Assembly Mechanisms in a Marine Dinoflagellate Bloom

2019 ◽  
Vol 85 (15) ◽  
Author(s):  
Jin Zhou ◽  
Guo-Fu Chen ◽  
Ke-Zhen Ying ◽  
Hui Jin ◽  
Jun-Ting Song ◽  
...  
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Stochastic Processes ◽  
Algal Bloom ◽  
Microbial Succession ◽  
Free Living ◽  
Environmental Selection ◽  
Deterministic Processes ◽  
Bacterial Groups ◽  
Living Bacteria

ABSTRACT Given the ecological significance of microorganisms in algal blooming events, it is critical to understand the mechanisms regarding their distribution under different conditions. We tested the hypothesis that microbial community succession is strongly associated with algal bloom stages, and that the assembly mechanisms are cocontrolled by deterministic and stochastic processes. Community structures and underlying ecological processes of microbial populations (attached and free-living bacteria) at three algal bloom stages (pre-, during, and postbloom) over a complete dinoflagellate Scrippsiella trochoidea bloom were investigated. Both attached and free-living taxa had a strong response to the bloom event, and the latter was more sensitive than the former. The contribution of environmental parameters to microbial variability was 40.2%. Interaction analysis showed that complex positive or negative correlation networks exist in phycosphere microbes. These relationships were the potential drivers of mutualist and competitive interactions that impacted bacterial succession. Null model analysis showed that the attached bacterial community primarily exhibited deterministic processes at pre- and during-bloom stages, while dispersal-related processes contributed to a greater extent at the postbloom stage. In the free-living bacterial community, homogeneous selection and dispersal limitation dominated in the initial phase, which gave way to more deterministic processes at the two later stages. Relative contribution analyses further demonstrated that the community turnover of attached bacteria was mainly driven by environmental selection, while stochastic factors had partial effects on the assembly of free-living bacteria. Taken together, these data demonstrated that a robust link exists between bacterioplankton community structure and bloom progression, and phycosphere microbial succession trajectories are cogoverned by both deterministic and random processes. IMPORTANCE Disentangling the mechanisms shaping bacterioplankton communities during a marine ecological event is a core concern for ecologists. Harmful algal bloom (HAB) is a typical ecological disaster, and its formation is significantly influenced by alga-bacterium interactions. Microbial community shifts during the HAB process are relatively well known. However, the assembly processes of microbial communities in an HAB are not fully understood, especially the relative influences of deterministic and stochastic processes. We therefore analyzed the relative contributions of deterministic and stochastic processes during an HAB event. Both free-living and attached bacterial groups had a dramatic response to the HAB, and the relative importance of determinism versus stochasticity varied between the two bacterial groups at various bloom stages. Environmental factors and biotic interactions were the main drivers impacting the microbial shift process. Our results strengthen the understanding of the ecological mechanisms controlling microbial community patterns during the HAB process.

Illuminating key microbial players and metabolic processes involved in the remineralization of particulate organic carbon in the ocean’s twilight zone by metaproteomics

2021 ◽  
Author(s):  
Ling-Fen Kong ◽  
Yan-Bin He ◽  
Zhang-Xian Xie ◽  
Xing Luo ◽  
Hao Zhang ◽  
...  
Keyword(s):  
Microbial Community ◽  
Organic Carbon ◽  
Particulate Organic Carbon ◽  
Hydrolytic Enzymes ◽  
Northwest Pacific ◽  
Twilight Zone ◽  
Metabolic Processes ◽  
Northwest Pacific Ocean ◽  
Niche Complementarity ◽  
Bacterial Groups

The twilight zone (from the base of the euphotic zone to the depth of 1000 m) is the major area of particulate organic carbon (POC) remineralization in the ocean, and heterotrophic microbes contribute to more than 70% of the estimated remineralization. However, little is known about the microbial community and metabolic activity directly associated with POC remineralization in this chronically understudied realm. Here, we characterized the microbial community proteomes of POCs collected from the twilight zone of three contrasting sites in the Northwest Pacific Ocean using a metaproteomic approach. The particle-attached bacteria from Alteromonadales, Rhodobacterales, and Enterobacteriales were the primary POC remineralizers. Hydrolytic enzymes, including proteases and hydrolases, that degrade proteinaceous components and polysaccharides, the main constituents of POC, were abundant and taxonomically associated with these bacterial groups. Furthermore, identification of diverse species-specific transporters and metabolic enzymes implied niche specialization for nutrient acquisition among these bacterial groups. Temperature was the main environmental factor driven the active bacterial groups and metabolic processes, and Enterobacteriales replaced Alteromonadales as the predominant group under low temperature. This study provides insight into the key bacteria and metabolic processes involved in POC remineralization, and niche complementarity and species substitution among bacterial groups are critical for efficient POC remineralization in the twilight zone. IMPORTANCE The Ocean’s twilight zone is a critical zone where more than 70% of the sinking particulate organic carbon (POC) are remineralized. Therefore, the twilight zone determines the size of biological carbon storage in the ocean, and regulates the global climate. Prokaryotes are major players that govern remineralization of POC in this region. However, knowledge of microbial community structure and metabolic activity is still lacking. This study unveiled microbial communities and metabolic activities of POCs collected from the twilight zone of three contrasting environments in the Northwest Pacific Ocean using a metaproteomic approach. Alteromonadales, Rhodobacterales and Enterobacteriales were the major remineralizers of POC. They excreted diverse species-specific hydrolytic enzymes to split POC to solubilized POC or dissolved organic carbon. Temperature played a crucial role in regulating the community composition and metabolism. Furthermore, niche complementarity or species substitution among bacterial groups guaranteed the efficient remineralization of POC in the twilight zone.

A peek in the micro-sized world: a review of design principles, engineering tools, and applications of engineered microbial community

2020 ◽  
Vol 48 (2) ◽  
pp. 399-409
Author(s):  
Baizhen Gao ◽  
Rushant Sabnis ◽  
Tommaso Costantini ◽  
Robert Jinkerson ◽  
Qing Sun
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Environmental Remediation ◽  
Real Life ◽  
Design Principles ◽  
Microbial Interactions ◽  
Potential Applications ◽  
New Gene ◽  
Global Biogeochemical Cycles ◽  
Synthetic Microbial Communities

Microbial communities drive diverse processes that impact nearly everything on this planet, from global biogeochemical cycles to human health. Harnessing the power of these microorganisms could provide solutions to many of the challenges that face society. However, naturally occurring microbial communities are not optimized for anthropogenic use. An emerging area of research is focusing on engineering synthetic microbial communities to carry out predefined functions. Microbial community engineers are applying design principles like top-down and bottom-up approaches to create synthetic microbial communities having a myriad of real-life applications in health care, disease prevention, and environmental remediation. Multiple genetic engineering tools and delivery approaches can be used to ‘knock-in' new gene functions into microbial communities. A systematic study of the microbial interactions, community assembling principles, and engineering tools are necessary for us to understand the microbial community and to better utilize them. Continued analysis and effort are required to further the current and potential applications of synthetic microbial communities.

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