scholarly journals Antibiotic resistome and microbial community structure during anaerobic co-digestion of food waste, paper and cardboard

2020 ◽  
Vol 96 (2) ◽  
Author(s):  
Kärt Kanger ◽  
Nigel G H Guilford ◽  
HyunWoo Lee ◽  
Camilla L Nesbø ◽  
Jaak Truu ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Solid State ◽  
Food Waste ◽  
Microbial Community Structure ◽  
Microbial Community Composition ◽  
Microbial Community Analysis ◽  
Waste Paper ◽  
Rrna Gene ◽  
Significant Shift

ABSTRACT Solid organic waste is a significant source of antibiotic resistance genes (ARGs) and effective treatment strategies are urgently required to limit the spread of antimicrobial resistance. Here, we studied ARG diversity and abundance as well as the relationship between antibiotic resistome and microbial community structure within a lab-scale solid-state anaerobic digester treating a mixture of food waste, paper and cardboard. A total of 10 samples from digester feed and digestion products were collected for microbial community analysis including small subunit rRNA gene sequencing, total community metagenome sequencing and high-throughput quantitative PCR. We observed a significant shift in microbial community composition and a reduction in ARG diversity and abundance after 6 weeks of digestion. ARGs were identified in all samples with multidrug resistance being the most abundant ARG type. Thirty-two per cent of ARGs detected in digester feed were located on plasmids indicating potential for horizontal gene transfer. Using metagenomic assembly and binning, we detected potential bacterial hosts of ARGs in digester feed, which included Erwinia, Bifidobacteriaceae, Lactococcus lactis and Lactobacillus. Our results indicate that the process of sequential solid-state anaerobic digestion of food waste, paper and cardboard tested herein provides a significant reduction in the relative abundance of ARGs per 16S rRNA gene.

scholarly journals Antibiotic resistome and microbial community structure during anaerobic co-digestion of food waste, paper and cardboard

2019 ◽  
Author(s):  
Kärt Kanger ◽  
Nigel G.H. Guilford ◽  
HyunWoo Lee ◽  
Camilla L. Nesbø ◽  
Jaak Truu ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Community Structure ◽  
Microbial Community ◽  
Food Waste ◽  
Microbial Community Structure ◽  
Organic Waste ◽  
Treatment Strategies ◽  
Antibiotic Resistance Genes ◽  
Waste Paper ◽  
Rrna Gene

ABSTRACTAntimicrobial resistance is a globally recognized public health risk. High incidence of antibiotic resistant bacteria and antibiotic resistance genes (ARGs) in solid organic waste necessitates the development of effective treatment strategies. The objective of this study was to assess ARG diversity and abundance as well as the relationship between resistome and microbial community structure during anaerobic co-digestion (AD) of food waste, paper and cardboard. A lab-scale solid-state AD system consisting of six sequentially fed leach beds (each with a solids retention time of 42 days) and an upflow anaerobic sludge blanket (UASB) reactor was operated under mesophilic conditions continuously for 88 weeks to successfully treat municipal organic waste and produce biogas. A total of ten samples from digester feed and digestion products were collected for microbial community analysis including SSU rRNA gene sequencing, total community metagenome sequencing and quantitative PCR. Taxonomic analyses revealed that AD changed the taxonomic profile of the microbial community: digester feed was dominated by bacterial and eukaryotic taxa while anaerobic digestate possessed a large proportion of archaea mainly belonging to the methanogenic genusMethanosaeta. ARGs were identified in all samples with significantly higher richness and relative abundance per 16S rRNA gene in digester feed compared to digestion products. Multidrug resistance was the most abundant ARG type. AD was not able to completely remove ARGs as shown by ARGs detected in digestion products. Using metagenomic assembly and binning we detected potential bacterial hosts of ARGs in digester feed, that includedErwinia, Bifidobacteriaceae, Lactococcus lactisandLactobacillus.IMPORTANCESolid organic waste is a significant source of antibiotic resistance genes (ARGs) (1) and effective treatment strategies are urgently required to limit the spread of antimicrobial resistance. Here we studied the antibiotic resistome and microbial community structure within an anaerobic digester treating a mixture of food waste, paper and cardboard. We observed a significant shift in microbial community composition and a reduction in ARG diversity and abundance after 6 weeks of digestion. We identified the host organisms of some of the ARGs including potentially pathogenic as well as non-pathogenic bacteria, and we detected mobile genetic elements required for horizontal gene transfer. Our results indicate that the process of sequential solid-state anaerobic digestion of food waste, paper and cardboard tested herein provides a significant reduction in the relative abundance of ARGs per 16S rRNA gene.

scholarly journals Subsurface Microbial Diversity in Deep-Granitic-Fracture Water in Colorado

2007 ◽  
Vol 74 (1) ◽  
pp. 143-152 ◽  
Author(s):  
Jason W. Sahl ◽  
Raleigh Schmidt ◽  
Elizabeth D. Swanner ◽  
Kevin W. Mandernack ◽  
Alexis S. Templeton ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Phospholipid Fatty Acid ◽  
Statistical Analyses ◽  
Microbial Community Analysis ◽  
Rrna Gene ◽  
Significant Shift ◽  
Clone Libraries ◽  
Borehole Water ◽  
Candidate Division

ABSTRACT A microbial community analysis using 16S rRNA gene sequencing was performed on borehole water and a granite rock core from Henderson Mine, a >1,000-meter-deep molybdenum mine near Empire, CO. Chemical analysis of borehole water at two separate depths (1,044 m and 1,004 m below the mine entrance) suggests that a sharp chemical gradient exists, likely from the mixing of two distinct subsurface fluids, one metal rich and one relatively dilute; this has created unique niches for microorganisms. The microbial community analyzed from filtered, oxic borehole water indicated an abundance of sequences from iron-oxidizing bacteria (Gallionella spp.) and was compared to the community from the same borehole after 2 weeks of being plugged with an expandable packer. Statistical analyses with UniFrac revealed a significant shift in community structure following the addition of the packer. Phospholipid fatty acid (PLFA) analysis suggested that Nitrosomonadales dominated the oxic borehole, while PLFAs indicative of anaerobic bacteria were most abundant in the samples from the plugged borehole. Microbial sequences were represented primarily by Firmicutes, Proteobacteria, and a lineage of sequences which did not group with any identified bacterial division; phylogenetic analyses confirmed the presence of a novel candidate division. This “Henderson candidate division” dominated the clone libraries from the dilute anoxic fluids. Sequences obtained from the granitic rock core (1,740 m below the surface) were represented by the divisions Proteobacteria (primarily the family Ralstoniaceae) and Firmicutes. Sequences grouping within Ralstoniaceae were also found in the clone libraries from metal-rich fluids yet were absent in more dilute fluids. Lineage-specific comparisons, combined with phylogenetic statistical analyses, show that geochemical variance has an important effect on microbial community structure in deep, subsurface systems.

scholarly journals Host–microbiome interactions in human type 2 diabetes following prebiotic fibre (galacto-oligosaccharide) intake

2016 ◽  
Vol 116 (11) ◽  
pp. 1869-1877 ◽  
Author(s):  
Camilla Pedersen ◽  
Edith Gallagher ◽  
Felicity Horton ◽  
Richard J. Ellis ◽  
Umer Z. Ijaz ◽  
...  
Keyword(s):  
Type 2 Diabetes ◽  
Community Structure ◽  
Microbial Community ◽  
Glucose Tolerance ◽  
Microbial Community Structure ◽  
Microbial Community Analysis ◽  
Intravenous Glucose ◽  
Intestinal Microbial Community ◽  
Human Type

AbstractAberrant microbiota composition and function have been linked to several pathologies, including type 2 diabetes. In animal models, prebiotics induce favourable changes in the intestinal microbiota, intestinal permeability (IP) and endotoxaemia, which are linked to concurrent improvement in glucose tolerance. This is the first study to investigate the link between IP, glucose tolerance and intestinal bacteria in human type 2 diabetes. In all, twenty-nine men with well-controlled type 2 diabetes were randomised to a prebiotic (galacto-oligosaccharide mixture) or placebo (maltodextrin) supplement (5·5 g/d for 12 weeks). Intestinal microbial community structure, IP, endotoxaemia, inflammatory markers and glucose tolerance were assessed at baseline and post intervention. IP was estimated by the urinary recovery of oral51Cr-EDTA and glucose tolerance by insulin-modified intravenous glucose tolerance test. Intestinal microbial community analysis was performed by high-throughput next-generation sequencing of 16S rRNA amplicons and quantitative PCR. Prebiotic fibre supplementation had no significant effects on clinical outcomes or bacterial abundances compared with placebo; however, changes in the bacterial family Veillonellaceae correlated inversely with changes in glucose response and IL-6 levels (r−0·90,P=0·042 for both) following prebiotic intake. The absence of significant changes to the microbial community structure at a prebiotic dosage/length of supplementation shown to be effective in healthy individuals is an important finding. We propose that concurrent metformin treatment and the high heterogeneity of human type 2 diabetes may have played a significant role. The current study does not provide evidence for the role of prebiotics in the treatment of type 2 diabetes.

scholarly journals Coupled changes in soil organic carbon fractions and microbial community composition in urban and suburban forests

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Xueying Zhang ◽  
Xiaomei Chen ◽  
Muying Liu ◽  
Zhanying Xu ◽  
Hui Wei
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Organic Carbon ◽  
Soil Organic Carbon ◽  
Community Composition ◽  
Microbial Community Structure ◽  
Soil Microorganisms ◽  
Microbial Community Composition ◽  
Soil C ◽  
Suburban Forests

Abstract Climate change and rapid urbanization have greatly impacted urban forest ecosystems and the carbon (C) cycle. To assess the effects of urbanization on forest soil C and soil microorganisms, six natural forests in a highly-urbanized region were selected as the research objects. Soil samples were collected to investigate the content and fractions of the soil organic carbon (SOC), as well as the soil microbial community composition. The results showed that the SOC content and fractions were substantially lower in the urban forests than in the suburban forests. Meanwhile, the total amount of phospholipid fatty acids (PLFAs) at suburban sites was twice more than that at urban sites, with shifts in microbial community structure. The potential differences in C inputs and nutrient limitation in urban forests may aggravate the low quantity and quality of SOC and consequently impact microbial community abundance and structure. Variation in microbial community structure was found to explain the loss of soil C pools by affecting the C inputs and promoting the decomposition of SOC. Therefore, the coupled changes in SOC and soil microorganisms induced by urbanization may adversely affect soil C sequestration in subtropical forests.

Changes in aerobic fermentation and microbial community structure in food waste derived from different dietary regimes

2020 ◽  
Vol 317 ◽  
pp. 123948
Author(s):  
Yanzeng Li ◽  
Zhou Chen ◽  
Yanyan Peng ◽  
Kaiming Zheng ◽  
Chengsong Ye ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Food Waste ◽  
Microbial Community Structure ◽  
Aerobic Fermentation

Spatial variation in microbial community structure, richness, and diversity in an alluvial aquifer

2012 ◽  
Vol 58 (9) ◽  
pp. 1135-1151 ◽  
Author(s):  
P.G. Medihala ◽  
J.R. Lawrence ◽  
G.D.W. Swerhone ◽  
D.R. Korber
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Spatial Variability ◽  
Microbial Communities ◽  
Microbial Community Structure ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Microbial Community Composition ◽  
Alluvial Aquifer ◽  
Gradient Gel Electrophoresis

Relatively little is known regarding the spatial variability of microbial communities in aquifers where well fouling is an issue. In this study 2 water wells were installed in an alluvial aquifer located adjacent to the North Saskatchewan River and an associated piezometer network developed to facilitate the study of microbial community structure, richness, and diversity. Carbon utilization data analysis revealed reduced microbial activity in waters collected close to the wells. Functional PCR and quantitative PCR analysis indicated spatial variability in the potential for iron-, sulphate-, and nitrate-reducing activity at all locations in the aquifer. Denaturing gradient gel electrophoresis analysis of aquifer water samples using principal components analyses indicated that the microbial community composition was spatially variable, and denaturing gradient gel electrophoresis sequence analysis revealed that bacteria belonging to the genera Acidovorax , Rhodobacter , and Sulfuricurvum were common throughout the aquifer. Shannon’s richness (H′) and Pielou’s evenness (J′) indices revealed a varied microbial diversity (H′ = 1.488–2.274) and an even distribution of microbial communities within the aquifer (J′ = 0.811–0.917). Overall, these analyses revealed that the aquifer’s microbial community varied spatially in terms of composition, richness, and metabolic activity. Such information may facilitate the diagnosis, prevention, and management of fouling.

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