scholarly journals Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant

2015 ◽  
Vol 6 ◽  
Author(s):  
Brandon Brooks ◽  
Ryan S. Mueller ◽  
Jacque C. Young ◽  
Michael J. Morowitz ◽  
Robert L. Hettich ◽  
...  
Keyword(s):  
Microbial Community ◽  
Gastrointestinal Tract ◽  
Preterm Infant ◽  
Aerobic And Anaerobic

scholarly journals Environmental parameters and microbial community profiles as indication towards microbial activities and diversity in aquaponic system compartments

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zala Schmautz ◽  
Carlos A. Espinal ◽  
Andrea M. Bohny ◽  
Fabio Rezzonico ◽  
Ranka Junge ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Profile Analysis ◽  
Operation Mode ◽  
Environmental Parameters ◽  
Plant Production ◽  
Microbial Activities ◽  
Anaerobic Processes ◽  
Abiotic Parameters ◽  
Aerobic And Anaerobic

Abstract Background An aquaponic system couples cultivation of plants and fish in the same aqueous medium. The system consists of interconnected compartments for fish rearing and plant production, as well as for water filtration, with all compartments hosting diverse microbial communities, which interact within the system. Due to the design, function and operation mode of the individual compartments, each of them exhibits unique biotic and abiotic conditions. Elucidating how these conditions shape microbial communities is useful in understanding how these compartments may affect the quality of the water, in which plants and fish are cultured. Results We investigated the possible relationships between microbial communities from biofilms and water quality parameters in different compartments of the aquaponic system. Biofilm samples were analyzed by total community profiling for bacterial and archaeal communities. The results implied that the oxygen levels could largely explain the main differences in abiotic parameters and microbial communities in each compartment of the system. Aerobic system compartments are highly biodiverse and work mostly as a nitrifying biofilter, whereas biofilms in the anaerobic compartments contain a less diverse community. Finally, the part of the system connecting the aerobic and anaerobic processes showed common conditions where both aerobic and anaerobic processes were observed. Conclusion Different predicted microbial activities for each compartment were found to be supported by the abiotic parameters, of which the oxygen saturation, total organic carbon and total nitrogen differentiated clearly between samples from the main aerobic loop and the anaerobic compartments. The latter was also confirmed using microbial community profile analysis.

scholarly journals Uncovering the Structure and Function of Microbial Communities Formed During Periodic Tilling of TNT and DNT Co-Contaminated Soils

2020 ◽  
Author(s):  
Saeed Keshani Langroodi ◽  
Yemin Lan ◽  
Ben Stenuit ◽  
Gail Rosen ◽  
Joseph B Hughes ◽  
...  
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Contaminated Soils ◽  
Bacterial Community Composition ◽  
Amplicon Sequencing ◽  
Metagenomic Data ◽  
Military Conflict ◽  
Nitro Explosives ◽  
And Function ◽  
Aerobic And Anaerobic

Environmental contamination by 2,4,6-trinitrotoluene (TNT), historically the most widely used secondary explosive, is a long-standing problem in former military conflict areas and at manufacturing and decommissioning plants. In field test plots at a former explosives manufacturing site, removal of TNT and dinitrotoluenes (DNTs) was observed following periods of tillage. Since tilling of soils has previously been shown to alter the microbial community, this study was aimed at understanding how the microbial community is altered in soils with historical contamination of nitro explosives from the former Barksdale TNT plant. Samples of untilled pristine soils, untilled TNT-contaminated soils and tilled TNT-contaminated soils were subjected to targeted amplicon sequencing of 16S ribosomal RNA genes in order to compare the structure of their bacterial communities. In addition, metagenomic data generated from the TNT tilled soil was used to understand the potential functions of the bacterial community relevant to nitroaromatic degradation. While the biodiversity dropped and the Burkholderiales order became dominant in both tilled and untilled soil regardless of tillage, the bacterial community composition at finer taxonomic levels revealed a greater difference between the two treatments. Functional analysis of metagenome assembled genome (MAG) bins through systematic review of commonly proposed DNT and TNT biotransformation pathways suggested that both aerobic and anaerobic degradation pathways were present. A proposed pathway that considers both aerobic and anaerobic steps in the degradation of TNT in the scenario of the tilled contaminated soils is presented.

scholarly journals Stunted childhood growth is associated with decompartmentalization of the gastrointestinal tract and overgrowth of oropharyngeal taxa

2018 ◽  
Vol 115 (36) ◽  
pp. E8489-E8498 ◽  
Author(s):  
Pascale Vonaesch ◽  
Evan Morien ◽  
Lova Andrianonimiadana ◽  
Hugues Sanke ◽  
Jean-Robert Mbecko ◽  
...  
Keyword(s):  
Small Intestine ◽  
Microbial Community ◽  
Gastrointestinal Tract ◽  
Bacterial Overgrowth ◽  
Oral Bacteria ◽  
Sub Saharan Africa ◽  
Growth Delay ◽  
Current View ◽  
Fecal Samples ◽  
Small Intestinal

Linear growth delay (stunting) affects roughly 155 million children under the age of 5 years worldwide. Treatment has been limited by a lack of understanding of the underlying pathophysiological mechanisms. Stunting is most likely associated with changes in the microbial community of the small intestine, a compartment vital for digestion and nutrient absorption. Efforts to better understand the pathophysiology have been hampered by difficulty of access to small intestinal fluids. Here, we describe the microbial community found in the upper gastrointestinal tract of stunted children aged 2–5 y living in sub-Saharan Africa. We studied 46 duodenal and 57 gastric samples from stunted children, as well as 404 fecal samples from stunted and nonstunted children living in Bangui, Central African Republic, and in Antananarivo, Madagascar, using 16S Illumina Amplicon sequencing and semiquantitative culture methods. The vast majority of the stunted children showed small intestinal bacterial overgrowth dominated by bacteria that normally reside in the oropharyngeal cavity. There was an overrepresentation of oral bacteria in fecal samples of stunted children, opening the way for developing noninvasive diagnostic markers. In addition, Escherichia coli/Shigella sp. and Campylobacter sp. were found to be more prevalent in stunted children, while Clostridia, well-known butyrate producers, were reduced. Our data suggest that stunting is associated with a microbiome “decompartmentalization” of the gastrointestinal tract characterized by an increased presence of oropharyngeal bacteria from the stomach to the colon, hence challenging the current view of stunting arising solely as a consequence of small intestine overstimulation through recurrent infections by enteric pathogens.

Characterization of Planktonic and Biofilm Communities of Day-of-Hatch Chicks Cecal Microflora and Their Resistance to Salmonella Colonization†

2009 ◽  
Vol 72 (5) ◽  
pp. 959-965 ◽  
Author(s):  
CYNTHIA L. SHEFFIELD ◽  
TAWNI L. CRIPPEN ◽  
KATHLEEN ANDREWS ◽  
ROY J. BONGAERTS ◽  
DAVID J. NISBET
Keyword(s):  
Microbial Community ◽  
Gastrointestinal Tract ◽  
Continuous Flow ◽  
Salmonella Enterica Serovar Typhimurium ◽  
Bacterial Species ◽  
Serovar Typhimurium ◽  
Automated Ribotyping ◽  
Cecal Microflora ◽  
Planktonic Communities

Recent concerns about the use of antimicrobials in food animals have increased interest in the microbial ecology and biofilms within their gastrointestinal tract. This work used a continuous-flow chemostat system to model the microbial community within the ceca from day-of-hatch chicks and its ability to resist colonization by Salmonella enterica serovar Typhimurium. We characterized the biofilm and planktonic communities from five cultures by using automated ribotyping. Eight species from six different genera were identified. Overall, the planktonic communities were more diverse, with 40% of the cultures containing four or more bacterial species. Eighty percent of the biofilm communities contained only one or two species of bacteria. Enterococcus faecalis was the only species isolated from all communities. None of the resulting microbial communities was able to resist colonization by S. enterica serovar Typhimurium. This is the first study to provide a molecular-based characterization of the biofilm and planktonic communities found in day-of-hatch chicken cecal microflora cultures.

Effects of poly-β-hydroxybutyrate (PHB) on Siberian sturgeon (Acipenser baerii) fingerlings performance and its gastrointestinal tract microbial community

2011 ◽  
Vol 79 (1) ◽  
pp. 25-33 ◽  
Author(s):  
Ebrahim H. Najdegerami ◽  
Tiet Ngoc Tran ◽  
Tom Defoirdt ◽  
Massimo Marzorati ◽  
Patrick Sorgeloos ◽  
...  
Keyword(s):  
Microbial Community ◽  
Gastrointestinal Tract ◽  
Siberian Sturgeon ◽  
Acipenser Baerii
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