scholarly journals Microorganisms Move a Short Distance into an Almond Orchard from an Adjacent Upwind Poultry Operation

2020 ◽  
Vol 86 (15) ◽  
Author(s):  
Christopher G. Theofel ◽  
Thomas R. Williams ◽  
Eduardo Gutierrez ◽  
Gordon R. Davidson ◽  
Michele Jay-Russell ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Foodborne Pathogens ◽  
Short Distance ◽  
Soil Surface ◽  
Plate Count ◽  
Rrna Gene ◽  
Content Type ◽  
Aerobic Plate Count ◽  
And Control ◽  
Almond Orchard

ABSTRACT Over a 2-year period, drag swabs of orchard soil surface and air, soil, and almond leaf samples were collected in an almond orchard adjacent to (35 m from the first row of trees) and downwind from a poultry operation and in two almond orchards (controls) that were surrounded by other orchards. Samples were evaluated for aerobic plate count, generic Escherichia coli, other coliforms, the presence of Salmonella, bacterial community structure (analyzed through sequencing of the 16S rRNA gene), and amounts of dry solids (dust) on leaf surfaces on trees 0, 60, and 120 m into each orchard. E. coli was isolated from 41 of 206 (20%) and 1 of 207 (0.48%) air samples in the almond-poultry and control orchards, respectively. Salmonella was not isolated from any of the 529 samples evaluated. On average, the amount of dry solids on leaves collected from trees closest to the poultry operation was more than 2-fold greater than from trees 120 m into the orchard or from any of the trees in the control orchards. Members of the family Staphylococcaceae—often associated with poultry—were, on average, significantly (P < 0.001) more abundant in the phyllosphere of trees closest to the poultry operation (10% of relative abundance) than in trees 120 m into the orchard (1.7% relative abundance) or from any of the trees in control orchards (0.41% relative abundance). Poultry-associated microorganisms from a commercial operation transferred a short distance into an adjacent downwind almond orchard. IMPORTANCE The movement of microorganisms, including foodborne pathogens, from animal operations into adjacent plant crop-growing environments is not well characterized. This study provides evidence that dust and bioaerosols moved from a commercial poultry operation a short distance downwind into an almond orchard and altered the microbiome recovered from the leaves. These data provide growers with information they can use to assess food safety risks on their property.

scholarly journals Duodenal-Mucosal Bacteria Associated with Celiac Disease in Children

2013 ◽  
Vol 79 (18) ◽  
pp. 5472-5479 ◽  
Author(s):  
Ester Sánchez ◽  
Ester Donat ◽  
Carmen Ribes-Koninckx ◽  
Maria Leonor Fernández-Murga ◽  
Yolanda Sanz
Keyword(s):  
Celiac Disease ◽  
Klebsiella Oxytoca ◽  
16S Rrna Gene Sequencing ◽  
Duodenal Mucosa ◽  
Plate Count ◽  
Rrna Gene ◽  
Content Type ◽  
Inflammatory Status ◽  
And Control ◽  
Active Disease

ABSTRACTCeliac disease (CD) is an immune-mediated enteropathy triggered by the ingestion of cereal gluten proteins. This disorder is associated with imbalances in the gut microbiota composition that could be involved in the pathogenesis of CD. The aim of this study was to characterize the composition and diversity of the cultivable duodenal mucosa-associated bacteria of CD patients and control children. Duodenal biopsy specimens from patients with active disease on a gluten-containing diet (n= 32), patients with nonactive disease after adherence to a gluten-free diet (n= 17), and controls (n= 8) were homogenized and plated on plate count agar, Wilkins-Chalgren agar, brain heart agar, or yeast, Casitone, and fatty acid agar. The isolates were identified by partial 16S rRNA gene sequencing. Renyi diversity profiles showed the highest diversity values for active CD patients, followed by nonactive CD patients and control individuals. Members of the phylumProteobacteriawere more abundant in patients with active CD than in the other child groups, while those of the phylumFirmicuteswere less abundant. Members of the familiesEnterobacteriaceaeandStaphylococcaceae, particularly the speciesKlebsiella oxytoca,Staphylococcus epidermidis, andStaphylococcus pasteuri, were more abundant in patients with active disease than in controls. In contrast, members of the familyStreptococcaceaewere less abundant in patients with active CD than in controls. Furthermore, isolates of theStreptococcus anginosusandStreptococcus mutansgroups were more abundant in controls than in both CD patient groups, regardless of inflammatory status. The findings indicated that the disease is associated with the overgrowth of possible pathobionts that exclude symbionts or commensals that are characteristic of the healthy small intestinal microbiota.

scholarly journals Lachnospiraceae and Bacteroidales Alternative Fecal Indicators Reveal Chronic Human Sewage Contamination in an Urban Harbor

2011 ◽  
Vol 77 (19) ◽  
pp. 6972-6981 ◽  
Author(s):  
Ryan J. Newton ◽  
Jessica L. VandeWalle ◽  
Mark A. Borchardt ◽  
Marc H. Gorelick ◽  
Sandra L. McLellan
Keyword(s):  
Sequence Analysis ◽  
Genetic Marker ◽  
Microbial Community Composition ◽  
Fold Increase ◽  
Fecal Pollution ◽  
Plate Count ◽  
Rrna Gene ◽  
Fecal Indicators ◽  
Fecal Indicator ◽  
Content Type

ABSTRACTThe complexity of fecal microbial communities and overlap among human and other animal sources have made it difficult to identify source-specific fecal indicator bacteria. However, the advent of next-generation sequencing technologies now provides increased sequencing power to resolve microbial community composition within and among environments. These data can be mined for information on source-specific phylotypes and/or assemblages of phylotypes (i.e., microbial signatures). We report the development of a new genetic marker for human fecal contamination identified through microbial pyrotag sequence analysis of the V6 region of the 16S rRNA gene. Sequence analysis of 37 sewage samples and comparison with database sequences revealed a human-associated phylotype within theLachnospiraceaefamily, which was closely related to the genusBlautia. This phylotype, termed Lachno2, was on average the second most abundant fecal bacterial phylotype in sewage influent samples from Milwaukee, WI. We developed a quantitative PCR (qPCR) assay for Lachno2 and used it along with the qPCR-based assays for humanBacteroidales(based on the HF183 genetic marker), totalBacteroidalesspp., and enterococci and the conventionalEscherichia coliand enterococci plate count assays to examine the prevalence of fecal and human fecal pollution in Milwaukee's harbor. Both the conventional fecal indicators and the human-associated indicators revealed chronic fecal pollution in the harbor, with significant increases following heavy rain events and combined sewer overflows. The two human-associated genetic marker abundances were tightly correlated in the harbor, a strong indication they target the same source (i.e., human sewage). Human adenoviruses were routinely detected under all conditions in the harbor, and the probability of their occurrence increased by 154% for every 10-fold increase in the human indicator concentration. Both Lachno2 and humanBacteroidalesincreased specificity to detect sewage compared to general indicators, and the relationship to a human pathogen group suggests that the use of these alternative indicators will improve assessments for human health risks in urban waters.

scholarly journals Impact of Substratum Surface on Microbial Community Structure and Treatment Performance in Biological Aerated Filters

2013 ◽  
Vol 80 (1) ◽  
pp. 177-183 ◽  
Author(s):  
Lavane Kim ◽  
Eulyn Pagaling ◽  
Yi Y. Zuo ◽  
Tao Yan
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Bacterial Species ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Property Change ◽  
And Control ◽  
Start Ups

ABSTRACTThe impact of substratum surface property change on biofilm community structure was investigated using laboratory biological aerated filter (BAF) reactors and molecular microbial community analysis. Two substratum surfaces that differed in surface properties were created via surface coating and used to develop biofilms in test (modified surface) and control (original surface) BAF reactors. Microbial community analysis by 16S rRNA gene-based PCR-denaturing gradient gel electrophoresis (DGGE) showed that the surface property change consistently resulted in distinct profiles of microbial populations during replicate reactor start-ups. Pyrosequencing of the bar-coded 16S rRNA gene amplicons surveyed more than 90% of the microbial diversity in the microbial communities and identified 72 unique bacterial species within 19 bacterial orders. Among the 19 orders of bacteria detected,BurkholderialesandRhodocyclalesof theBetaproteobacteriaclass were numerically dominant and accounted for 90.5 to 97.4% of the sequence reads, and their relative abundances in the test and control BAF reactors were different in consistent patterns during the two reactor start-ups. Three of the five dominant bacterial species also showed consistent relative abundance changes between the test and control BAF reactors. The different biofilm microbial communities led to different treatment efficiencies, with consistently higher total organic carbon (TOC) removal in the test reactor than in the control reactor. Further understanding of how surface properties affect biofilm microbial communities and functional performance would enable the rational design of new generations of substrata for the improvement of biofilm-based biological treatment processes.

scholarly journals Faecal bacterial composition in horses with and without free faecal liquid: a case control study

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Katrin M. Lindroth ◽  
Johan Dicksved ◽  
Erik Pelve ◽  
Viveca Båverud ◽  
Cecilia E. Müller
Keyword(s):  
Relative Abundance ◽  
Case Control Study ◽  
Sampling Period ◽  
Rrna Gene ◽  
Bacterial Composition ◽  
Clostridioides Difficile ◽  
Liquid Phases ◽  
And Control ◽  
The 16S Rrna Gene ◽  
Control Study

AbstractFree faecal liquid (FFL) is a condition in horses which manifests as differential defecation of solid and liquid phases of faeces. The etiology of FFL is currently unknown, but deviances in the hindgut microbiota has been suggested to be of importance. The present study aimed to compare the faecal bacterial composition of farm-matched horses with (case, n = 50) and without (control, n = 50) FFL. Samples were collected at three different occasions. The V3 and V4 regions of the 16S rRNA gene were amplified and sequenced using Illumina sequencing. Also, samples were cultivated for detection of Clostridioides difficile and Clostridium perfringens. Analysis revealed similar faecal bacterial composition between case and control horses, but an effect of sampling period (p = 0.0001). Within sampling periods, 14 genera were present in higher or lower proportions in case compared to control horses in at least one sampling period. Compared to controls, case horses had higher relative abundance of Alloprevotella (adjusted p < 0.04) and lower relative abundance of Bacillus spp. (adjusted p < 0.03) in at least two sampling periods. All horses tested negative for C. difficile and C. perfringens by culture of faeces. Further studies are required to establish the clinical relevance of specific bacterial taxa in FFL.

Survey of the Bacterial Populations of Bologna Products1,2

1978 ◽  
Vol 41 (9) ◽  
pp. 692-695 ◽  
Author(s):  
JOHN T. FRUIN ◽  
JAMES F. FOSTER ◽  
JAMES L. FOWLER
Keyword(s):  
Escherichia Coli ◽  
Staphylococcus Aureus ◽  
Foodborne Pathogens ◽  
High Volume ◽  
Plate Count ◽  
Retail Market ◽  
Bacterial Populations ◽  
Retail Markets ◽  
Aerobic Plate Count

Bologna products most frequently are stored and consumed as refrigerated products. Thus bacteria that survive processing or those that contaminate the product subsequent to processing are not destroyed. Ten types of presliced, vacuum-packaged bologna products were purchased from a high-volume retail market and analyzed for total aerobic plate count (APC) and common foodborne pathogens. No Salmonella were isolated. Less than 1% of the 419 samples analyzed contained either Clostridium perfringens or Escherichia coli, Staphylococcus aureus was isolated from 4% of the samples, but only one sample contained more than 1000/g. Just over 5% of the samples contained coliform organisms. The manufacturer appeared to play an important role in bacterial quality of the finished items. An APC &lt; 5 × 106/g is a realistic criterion for bologna products at the time of delivery to retail markets.

scholarly journals Impact of Biochar Application to Soil on the Root-Associated Bacterial Community Structure of Fully Developed Greenhouse Pepper Plants

2011 ◽  
Vol 77 (14) ◽  
pp. 4924-4930 ◽  
Author(s):  
Max Kolton ◽  
Yael Meller Harel ◽  
Zohar Pasternak ◽  
Ellen R. Graber ◽  
Yigal Elad ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
Relative Abundance ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Community Composition ◽  
Systemic Resistance ◽  
Rrna Gene ◽  
Molecular Fingerprinting ◽  
Content Type ◽  
Biochar Amendment

ABSTRACTAdding biochar to soil has environmental and agricultural potential due to its long-term carbon sequestration capacity and its ability to improve crop productivity. Recent studies have demonstrated that soil-applied biochar promotes the systemic resistance of plants to several prominent foliar pathogens. One potential mechanism for this phenomenon is root-associated microbial elicitors whose presence is somehow augmented in the biochar-amended soils. The objective of this study was to assess the effect of biochar amendment on the root-associated bacterial community composition of mature sweet pepper (Capsicum annuumL.) plants. Molecular fingerprinting (denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphism) of 16S rRNA gene fragments showed a clear differentiation between the root-associated bacterial community structures of biochar-amended and control plants. The pyrosequencing of 16S rRNA amplicons from the rhizoplane of both treatments generated a total of 20,142 sequences, 92 to 95% of which were affiliated with theProteobacteria,Bacteroidetes,Actinobacteria, andFirmicutesphyla. The relative abundance of members of theBacteroidetesphylum increased from 12 to 30% as a result of biochar amendment, while that of theProteobacteriadecreased from 71 to 47%. TheBacteroidetes-affiliatedFlavobacteriumwas the strongest biochar-induced genus. The relative abundance of this group increased from 4.2% of total root-associated operational taxonomic units (OTUs) in control samples to 19.6% in biochar-amended samples. Additional biochar-induced genera included chitin and cellulose degraders (ChitinophagaandCellvibrio, respectively) and aromatic compound degraders (HydrogenophagaandDechloromonas). We hypothesize that these biochar-augmented genera may be at least partially responsible for the beneficial effect of biochar amendment on plant growth and viability.

Comparison of a Four-Section Spindle and Stomacher for Efficacy of Detaching Microorganisms from Fresh Vegetables

2015 ◽  
Vol 78 (7) ◽  
pp. 1380-1386 ◽  
Author(s):  
DO-KYUN KIM ◽  
SOO-JI KIM ◽  
DONG-HYUN KANG
Keyword(s):  
Foodborne Pathogens ◽  
Food Samples ◽  
Plate Count ◽  
Microbiological Analysis ◽  
Vegetable Samples ◽  
Fresh Vegetable ◽  
Detection Analysis ◽  
Fresh Vegetables ◽  
The Difference ◽  
Aerobic Plate Count

This study was undertaken to compare the effect of the spindle and stomacher for detaching microorganisms from fresh vegetables. The spindle is an apparatus for detaching microorganisms from food surfaces, which was developed in our laboratory. When processed with the spindle, food samples were barely disrupted, the original shape was maintained, and the diluent was clear, facilitating further detection analysis more easily than with stomacher treatment. The four-section spindle consists of four sample bag containers (A, B, C, and D) to economize time and effort by simultaneously processing four samples. The aerobic plate counts (APC) of 50 fresh vegetable samples were measured following spindle and stomacher treatment. Correlations between the two methods for each section of the spindle and stomacher were very high (R2 = 0.9828 [spindle compartment A; Sp A], 0.9855 [Sp B], 0.9848 [Sp C], and 0.9851 [Sp D]). One-tenth milliliter of foodborne pathogens suspensions was inoculated onto surfaces of food samples, and ratios of spindle-to-stomacher enumerations were close to 1.00 log CFU/g between every section of the spindle and stomacher. One of the greatest features of the spindle is that it can treat large-sized samples that exceed 200 g. Uncut whole apples, green peppers, potatoes, and tomatoes were processed by the spindle and by hand massaging by 2 min. Large-sized samples were also assayed for aerobic plate count and recovery of the three foodborne pathogens, and the difference between each section of the spindle and hand massaging was not significant (P &gt; 0.05). This study demonstrated that the spindle apparatus can be an alternative device for detaching microorganisms from all fresh vegetable samples for microbiological analysis by the food processing industry.

scholarly journals Microbiomes of Unreactive and Pathologically Altered Ileocecal Lymph Nodes of Slaughter Pigs

2013 ◽  
Vol 80 (1) ◽  
pp. 193-203 ◽  
Author(s):  
Evelyne Mann ◽  
Monika Dzieciol ◽  
Barbara U. Metzler-Zebeli ◽  
Martin Wagner ◽  
Stephan Schmitz-Esser
Keyword(s):  
Lymph Nodes ◽  
Rrna Gene ◽  
Content Type ◽  
Host Interactions ◽  
Zoonotic Risk ◽  
Slaughter Pigs ◽  
Associated Sequences ◽  
Relative Abundances ◽  
Reactive Hyperplasia ◽  
And Control

ABSTRACTMicrobe-laden dendritic cells are shifted to ileocecal lymph nodes (ICLNs), where microbes are concentrated and an adequate immune response is triggered. Hence, ICLNs are at a crucial position in immune anatomy and control processes of the local immune system. Pathological alterations in ICLNs, such as reactive hyperplasia,lymphadenitis purulenta, orgranulomatosa, can harbor a multitude of pathogens and commensals, posing a potential zoonotic risk in animal production. The aim of this study was to characterize the microbial diversity of unreactive ICLNs of slaughter pigs and to investigate community shifts in reactive ICLNs altered by enlargement, purulence, or granulomatous formations. Pyrosequencing of 16S rRNA gene amplicons from 32 ICLNs yielded 175,313 sequences, clustering into 650 operational taxonomic units (OTUs). OTUs were assigned to 239 genera and 11 phyla. Besides a highly diverse bacterial community in ICLNs, we observed significant shifts in pathologically altered ICLNs. The relative abundances ofCloacibacterium- andNovosphingobium-associated OTUs and the genusFaecalibacteriumwere significantly higher in unreactive ICLNs than in pathologically altered ICLNs. Enlarged ICLNs harbored significantly moreLactobacillus- andClostridium-associated sequences. Relative abundances ofMycoplasma,Bacteroides,Veillonella, andVariovoraxOTUs were significantly increased in granulomatous ICLNs, whereas abundances ofPseudomonas,Escherichia, andAcinetobacterOTUs were significantly increased in purulent ICLNs (P< 0.05). Correlation-based networks revealed interactions among OTUs in all ICLN groups, and discriminant analyses depicted discrimination in response to pathological alterations. This study is the first community-based survey in ICLNs of livestock animals and will provide a basis to broaden the knowledge of microbe-host interactions in pigs.

scholarly journals Few Highly Abundant Operational Taxonomic Units Dominate within Rumen Methanogenic Archaeal Species in New Zealand Sheep and Cattle

2014 ◽  
Vol 81 (3) ◽  
pp. 986-995 ◽  
Author(s):  
Henning Seedorf ◽  
Sandra Kittelmann ◽  
Peter H. Janssen
Keyword(s):  
New Zealand ◽  
Standard Deviation ◽  
Relative Abundance ◽  
Animal Feed ◽  
Rrna Gene ◽  
Content Type ◽  
Operational Taxonomic Units ◽  
Archaeal Species ◽  
Methanogen Community ◽  
Rumen Methanogen

ABSTRACTSequencing and analyses of 16S rRNA gene amplicons were performed to estimate the composition of the rumen methanogen community in 252 samples from eight cohorts of sheep and cattle, separated into 16 different sample groups by diet, and to determine which methanogens are most prominent in the rumens of farmed New Zealand ruminants.Methanobacteriales(relative abundance ± standard deviation, 89.6% ± 9.8%) andMethanomassiliicoccales(10.4% ± 9.8%) were the two major orders and contributed 99.98% (±0.1%) to the rumen methanogen communities in the samples. Sequences fromMethanobacterialeswere almost entirely from only four different species (or clades of very closely related species). Each was detectable in at least 89% of the samples. These four species or clades were theMethanobrevibacter gottschalkiiclade andMethanobrevibacter ruminantiumclade with a mean abundance of 42.4% (±19.5% standard deviation) and 32.9% (±18.8%), respectively, andMethanosphaerasp. ISO3-F5 (8.2% ± 6.7%) andMethanosphaerasp. group5 (5.6% ± 5.7%). These four species or clades appeared to be primarily represented by only one or, in one case, two dominant sequence types per species or clade when the sequences were grouped into operational taxonomic units (OTUs) at 99% sequence identity. The mean relative abundance ofMethanomassiliicoccalesin the samples was relatively low but exceeded 40% in some of the treatment groups. Animal feed affected the apparent methanogen community structure of both orders, as evident from differences in relative abundances of the major OTUs in animals under different feeding regimens.

Microbiological Quality of Shawarma in Saudi Arabia

1985 ◽  
Vol 48 (9) ◽  
pp. 811-814 ◽  
Author(s):  
M. AYAZ ◽  
F. A. OTHMAN ◽  
T. O. BAHARETH ◽  
A. M. AL-SOGAIR ◽  
W. N. SAWAYA
Keyword(s):  
Saudi Arabia ◽  
Foodborne Pathogens ◽  
Fast Food ◽  
Health Hazard ◽  
Microbiological Quality ◽  
Plate Count ◽  
Standard Procedures ◽  
Fast Food Restaurants ◽  
Aerobic Plate Count ◽  
Meat Samples

A total of 108 shawarma (cooked meat) samples were aseptically collected from various fast-food restaurants in Riyadh, Saudi Arabia. These samples were examined by standard procedures for determination of aerobic plate count (APC), and counts of coliforms, Staphylococcus aureus, Clostridium perfringens, and the detection of salmonellae. The APC ranged from 102 to 3.0 × 108 CFU/g. The counts for coliforms, S. aureus and C. perfringens ranged from &lt;10 to 106, &lt;10 to 105 and &lt;10 to 106 CFU/g, respectively. Twelve percent of the shawarma samples was positive for Salmonella. The results of this investigation indicate that foodborne pathogens present in shawarmas constitute a potential public health hazard.

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