scholarly journals Investigation of Sources, Diversity, and Variability of Bacterial Aerosols in Athens, Greece: A Pilot Study

Atmosphere ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 45
Author(s):  
Angelina Metaxatos ◽  
Sydonia Manibusan ◽  
Gediminas Mainelis
Keyword(s):  
Field Application ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Airborne Bacteria ◽  
Urban Air ◽  
Operational Taxonomic Units ◽  
Bacterial Aerosol ◽  
Bacterial Aerosols ◽  
Taxonomic Categories

We characterized the composition, diversity, and potential bacterial aerosol sources in Athens’ urban air by DNA barcoding (analysis of 16S rRNA genes) during three seasons in 2019. Air samples were collected using the recently developed Rutgers Electrostatic Passive Sampler (REPS). It is the first field application of REPS to study bacterial aerosol diversity. REPS samplers captured a sufficient amount of biological material to demonstrate the diversity of airborne bacteria and their variability over time. Overall, in the air of Athens, we detected 793 operational taxonomic units (OTUs), which were fully classified into the six distinct taxonomic categories (Phylum, Class, Order, etc.). These OTUs belonged to Phyla Actinobacteria, Firmicutes, Proteobacteria, Bacteroidetes, Cyanobacteria, and Fusobacteria. We found a complex community of bacterial aerosols with several opportunistic or potential pathogens in Athens’ urban air. Referring to the available literature, we discuss the likely sources of observed airborne bacteria, including soil, plants, animals, and humans. Our results on bacterial diversity are comparable to earlier studies, even though the sampling sites are different or geographically distant. However, the exact functional and ecological role of bioaerosols and, even more importantly, their impact on public health and the ecosystem requires further air monitoring and analysis.

scholarly journals Investigation of sources, diversity, and variability of bacterial aerosols in Athens, Greece: a pilot study

2021 ◽  
Author(s):  
Angelina Metaxatos ◽  
Sydonia Manibusan ◽  
Gediminas Mainelis
Keyword(s):  
Field Application ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Airborne Bacteria ◽  
Bacterial Composition ◽  
Commensal Microbiota ◽  
High Prevalence ◽  
Bacterial Aerosols ◽  
The Impact ◽  
Over Time

Abstract This study is the first attempt to describe the composition, diversity, and potential sources of bacterial aerosols in the urban air of Athens by DNA barcoding (analysis of 16S rRNA genes). It is also the first field application of the recently developed Rutgers Electrostatic Passive Sampler (REPS) to study the microbial diversity of aerosols. Three sampling campaigns 6–10 days in duration were conducted in the summer and fall of 2019. The completely passive REPS captured a sufficient amount of biological material to demonstrate the diversity of airborne bacteria and their variability over time. Overall, in the air of Athens, 793 OTUs were detected. Firmicutes, Proteobacteria, and Actinobacteria were the dominant Phyla, while the Cyanobacteria, Bacteroidetes, and Fusobacteria were the minor Phyla. The observed Phyla were further classified into 54 families. The families with high prevalence across our samples contained genera known to have pathogenic species, e.g., Streptococcus, Corynebacterium, Gemella, Pseudomonas, Staphylococcus, Neisseria; many species belonging to human or animal commensal microbiota were also detected. The paper discusses the likely sources of observed airborne bacteria, including soil, plants, animals, humans. Given the variability in bacterial composition over time, it is obvious that the contribution of those sources to airborne microbiota is dynamic. However, a more accurate linkage between the sources and airborne bacteria requires further study. Also, the exact functional and ecological role and, even more importantly, the impact of observed bacterial aerosols on public health and the ecosystem is still unknown and required further analysis.

scholarly journals Role of Broiler Carcasses and Processing Plant Air in Contamination of Modified-Atmosphere-Packaged Broiler Products with Psychrotrophic Lactic Acid Bacteria

2006 ◽  
Vol 73 (4) ◽  
pp. 1136-1145 ◽  
Author(s):  
Elina Vihavainen ◽  
Hanna-Saara Lundstr�m ◽  
Tuija Susiluoto ◽  
Joanna Koort ◽  
Lars Paulin ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
23S Rrna ◽  
Processing Plant ◽  
Modified Atmosphere ◽  
Production Plant ◽  
Meat Spoilage

ABSTRACT Some psychrotrophic lactic acid bacteria (LAB) are specific meat spoilage organisms in modified-atmosphere-packaged (MAP), cold-stored meat products. To determine if incoming broilers or the production plant environment is a source of spoilage LAB, a total of 86, 122, and 447 LAB isolates from broiler carcasses, production plant air, and MAP broiler products, respectively, were characterized using a library of HindIII restriction fragment length polymorphism (RFLP) patterns of the 16 and 23S rRNA genes as operational taxonomic units in numerical analyses. Six hundred thirteen LAB isolates from the total of 655 clustered in 29 groups considered to be species specific. Sixty-four percent of product isolates clustered either with Carnobacterium divergens or with Carnobacterium maltaromaticum type strains. The third major product-associated cluster (17% of isolates) was formed by unknown LAB. Representative strains from these three clusters were analyzed for the phylogeny of their 16S rRNA genes. This analysis verified that the two largest RFLP clusters consisted of carnobacteria and showed that the unknown LAB group consisted of Lactococcus spp. No product-associated LAB were detected in broiler carcasses sampled at the beginning of slaughter, whereas carnobacteria and lactococci, along with some other specific meat spoilage LAB, were recovered from processing plant air at many sites. This study reveals that incoming broiler chickens are not major sources of psychrotrophic spoilage LAB, whereas the detection of these organisms from the air of the processing environment highlights the role of processing facilities as sources of LAB contamination.

scholarly journals Treatment nonresponse in children receiving silver diamine fluoride for caries: A pilot study

2020 ◽  
Author(s):  
Ryan Richard Ruff ◽  
Bidisha Paul ◽  
Maria A Sierra ◽  
Fangxi Xu ◽  
Yasmi Crystal ◽  
...  
Keyword(s):  
Pilot Study ◽  
Bacterial Species ◽  
Illumina Miseq ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Lasso Regression ◽  
Silver Diamine Fluoride ◽  
Operational Taxonomic Units ◽  
Acid Tolerant ◽  
Nonsurgical Therapy

AbstractObjectives: Silver diamine fluoride (SDF) is a nonsurgical therapy for the arrest and prevention of dental caries with demonstrated clinical efficacy. Approximately 20% of children receiving SDF fail to respond to treatment. The objective of this study was to develop a predictive model of treatment nonresponse using machine learning. Methods: An observational pilot study (N=20) consisting of children with and without active decay and who did and did not respond to silver diamine fluoride provided salivary samples and plaque from infected and contralateral sites. 16S rRNA genes from samples were amplified and sequenced on an Illumina Miseq and analyzed using QIIME. The association between operational taxonomic units and treatment nonresponse was assessed using lasso regression and artificial neural networks. Results: Bivariate group comparisons of bacterial abundance indicate a number of genera were significantly different between nonresponders and those who responded to SDF therapy. No differences were found between nonresponders and caries-active subjects. Prevotella pallens and Veillonella denticariosi were retained in full lasso models and combined with clinical variables in a six-input multilayer perceptron. Discussion: The acidogenic and acid-tolerant nature of retained bacterial species may overcome the antimicrobial effects of SDF. Further research to validate the model in larger external samples is needed.

scholarly journals Coaggregation among Nonflocculating Bacteria Isolated from Activated Sludge

2003 ◽  
Vol 69 (10) ◽  
pp. 6056-6063 ◽  
Author(s):  
Anushree Malik ◽  
Masashi Sakamoto ◽  
Shohei Hanazaki ◽  
Masamitsu Osawa ◽  
Takanori Suzuki ◽  
...  
Keyword(s):  
16S Rrna ◽  
Activated Sludge ◽  
Aggregate Size ◽  
Spectrophotometric Assay ◽  
Full Length ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Acinetobacter Junii ◽  
Acinetobacter Johnsonii

ABSTRACT Thirty-two strains of nonflocculating bacteria isolated from sewage-activated sludge were tested by a spectrophotometric assay for their ability to coaggregate with one other in two-membered systems. Among these strains, eight showed significant (74 to 99%) coaggregation with Acinetobacter johnsonii S35 while only four strains coaggregated, to a lesser extent (43 to 65%), with Acinetobacter junii S33. The extent and pattern of coaggregation as well as the aggregate size showed good correlation with cellular characteristics of the coaggregating partners. These strains were identified by sequencing of full-length 16S rRNA genes. A. johnsonii S35 could coaggregate with strains of several genera, such as Oligotropha carboxidovorans, Microbacterium esteraromaticum, and Xanthomonas spp. The role of Acinetobacter isolates as bridging organisms in multigeneric coaggregates is indicated. This investigation revealed the role of much-neglected nonflocculating bacteria in floc formation in activated sludge.

scholarly journals The Xylella fastidiosa-Resistant Olive Cultivar “Leccino” Has Stable Endophytic Microbiota during the Olive Quick Decline Syndrome (OQDS)

Pathogens ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 35 ◽  
Author(s):  
Marzia Vergine ◽  
Joana B. Meyer ◽  
Massimiliano Cardinale ◽  
Erika Sabella ◽  
Martin Hartmann ◽  
...  
Keyword(s):  
Xylella Fastidiosa ◽  
Resistance Mechanisms ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Olive Cultivar ◽  
Olive Quick Decline Syndrome ◽  
Olive Trees ◽  
Potential Interactions ◽  
Highly Virulent

Xylella fastidiosa is a highly virulent pathogen that causes Olive Quick Decline Syndrome (OQDS), which is currently devastating olive plantations in the Salento region (Apulia, Southern Italy). We explored the microbiome associated with X. fastidiosa-infected (Xf-infected) and -uninfected (Xf-uninfected) olive trees in Salento, to assess the level of dysbiosis and to get first insights into the potential role of microbial endophytes in protecting the host from the disease. The resistant cultivar “Leccino” was compared to the susceptible cultivar “Cellina di Nardò”, in order to identify microbial taxa and parameters potentially involved in resistance mechanisms. Metabarcoding of 16S rRNA genes and fungal ITS2 was used to characterize both total and endophytic microbiota in olive branches and leaves. “Cellina di Nardò” showed a drastic dysbiosis after X. fastidiosa infection, while “Leccino” (both infected and uninfected) maintained a similar microbiota. The genus Pseudomonas dominated all “Leccino” and Xf-uninfected “Cellina di Nardò” trees, whereas Ammoniphilus prevailed in Xf-infected “Cellina di Nardò”. Diversity of microbiota in Xf-uninfected “Leccino” was higher than in Xf-uninfected “Cellina di Nardò”. Several bacterial taxa specifically associated with “Leccino” showed potential interactions with X. fastidiosa. The maintenance of a healthy microbiota with higher diversity and the presence of cultivar-specific microbes might support the resistance of “Leccino” to X. fastidiosa. Such beneficial bacteria might be isolated in the future for biological treatment of the OQDS.

scholarly journals Disturbance During Biofilm Community Succession Promotes Cooperation and Diversity

2018 ◽  
Author(s):  
James P. Stratford ◽  
Douglas M. Hodgson ◽  
Nelli J. Beecroft ◽  
Ann Smith ◽  
Julian R. Marchesi ◽  
...  
Keyword(s):  
Time Course ◽  
Explanatory Power ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Widespread Application ◽  
Operational Taxonomic Units ◽  
Microbial Biofilms ◽  
Macro Scale ◽  
First Time ◽  
High Diversity

AbstractDiversity-disturbance relationships have found widespread application in ecology, conservation and biodiversity management. In spite of their explanatory power, these conceptual frameworks have yet to be systematically applied to understanding succession in diverse microbial biofilms. Here we investigate community assembly in biofilms formed in replicate microbial bioelectrochemical systems using time-course sequencing of community 16S rRNA genes, corresponding to hundreds of operational taxonomic units (OTUs). For the first time we present a statistical model showing that a simple diversity-disturbance relationship can be used to explain dynamic changes in high diversity biofilm communities. This simple model reveals that succession in these systems is guided towards either a low diversity, generalist-dominated biofilm or a high diversity, cooperative-specialist biofilm, depending on the level of endogenous disturbance measured within the community. The pattern observed shows remarkable symmetry with findings from macro-scale communities such as grasslands, forests and coral reefs.

Analysis of the Salivary Microbiome in the Periodontal Disease patients with hypertension and non-hypertension

2020 ◽  
Vol 15 ◽  
Author(s):  
Suhua Li ◽  
Rexidan Zaker ◽  
Xueqian Chu ◽  
Reyida Asihati ◽  
Chong Li ◽  
...  
Keyword(s):  
Periodontal Disease ◽  
Anaerobic Bacteria ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Oral Microbiota ◽  
Periodontal Health ◽  
Differential Abundance ◽  
Operational Taxonomic Units ◽  
Hypervariable Regions ◽  
Microbiota Diversity

Background: An improved comprehension of the oral microbiota function in the pathogenesis of disease will contribute to diagnosis and treatment for both hypertension and periodontal disease. In our study, a comparison of the salivary microbiome between hypertension and Non-hypertension cohorts was designed to reveal microbial signatures. <P> Methods: Patients were divided into four sub-groups: Gingivitis, Periodontitis (stage 2, 3 and 4). Then the hypertension and Non-hypertension cohorts were split into periodontal health and periodontitis subgroups. The salivary samples were processed for DNA extraction (n=246). The V3-V4 hypervariable regions of microbiome 16S rRNA genes were amplified. Finally, sequencing libraries was constructed and subjected them to bioinformatics and statistical analyses. <P> Results: The oral microbial diversity decreased in both hypertension and periodontal disease groups compared to the healthy. At the genus level, the diversity showed 100 different operational taxonomic units (OTUs) for differential abundance testing. The first trend showed OTUs decreased in relative abundance with increasing periodontal disease, and as well as hypertension groups and non-hypertensive. For this trend OTUs comprised a mix of primarily anaerobic commensals and potential acute diarrhea pathogens. The second trend was that the diversity of genera was decreased in hypertension relative to non-hypertension, including other anaerobic bacteria related with periodontal disease. <P> Conclusions: Microbiota diversity decreased in both hypertension and different stages of periodontal disease groups, however, Neisseria and Solobacterium genera increased in co-existing hypertension and periodontal disease. Obviously, these findings indicate that the abundance of genera continues to change due to additional stresses caused by co-existing conditions

scholarly journals Identification of differential duodenal gene expression levels and microbiota abundance correlated with differences in energy utilisation in chickens

2013 ◽  
Vol 53 (12) ◽  
pp. 1269 ◽  
Author(s):  
Barbara M. Konsak ◽  
Dragana Stanley ◽  
Volker R. Haring ◽  
Mark S. Geier ◽  
Robert J. Hughes ◽  
...  
Keyword(s):  
Gene Expression ◽  
High Throughput Sequencing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Lactobacillus Species ◽  
Operational Taxonomic Units ◽  
Similar Genetic Background ◽  
The Difference ◽  
Production Animals ◽  
Utilisation Efficiency

Among the terrestrial production animals, chickens are the most efficient users of energy. Apparent metabolisable energy (AME) is a measure of energy utilisation efficiency representing the difference between energy consumed and energy lost via the excreta. There are significant differences in the energy utilisation capability of individual birds that have a similar genetic background and are raised under identical conditions. It would be of benefit to poultry producers if the basis of these differences could be understood and the differences minimised. We analysed duodenal gene expression and microbiota differences in birds with different energy utilisation efficiencies. Using microarray analysis, significant differences were found in duodenal gene expression between high- and low-AME birds, indicating that level of cell turnover may distinguish different groups of birds. High-throughput sequencing of bacterial 16S rRNA genes indicated that duodenal microbiota was dominated by Lactobacillus species and two operational taxonomic units, identified as lactobacilli species, were found to be more abundant (P < 0.05) in low-AME birds. The present study has identified gene expression and microbiota properties that correlate with differences in AME; further studies will be required to investigate the causal relationships.

scholarly journals Bacteria Associated with Mucus and Tissues of the Coral Oculina patagonica in Summer and Winter

2006 ◽  
Vol 72 (8) ◽  
pp. 5254-5259 ◽  
Author(s):  
Omry Koren ◽  
Eugene Rosenberg
Keyword(s):  
16S Rrna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Culturable Bacteria ◽  
Vibrio Splendidus ◽  
Marine Agar ◽  
Tissue Samples ◽  
Operational Taxonomic Units ◽  
Sybr Gold ◽  
16S Rrna Clone Library

ABSTRACT The relative abundance of bacteria in the mucus and crushed tissue of the Mediterranean coral Oculina patagonica was determined by analyses of the 16S rRNA genes of isolated colonies and from a 16S rRNA clone library of extracted DNA. By SYBR gold staining, the numbers of bacteria in mucus and tissue samples were 6.2 × 107 and 8.3 × 108/cm2 of coral surface, respectively, 99.8% of which failed to produce colonies on Marine Agar. From analysis of mucus DNA, the most-abundant bacterium was Vibrio splendidus, representing 68% and 50% of the clones from the winter and summer, respectively. After removal of mucus from coral by centrifugation, analyses of DNA from the crushed tissue revealed a large diversity of bacteria, with Vibrio species representing less than 5% of the clones. The most-abundant culturable bacteria were a Pseudomonas sp. (8 to 14%) and two different α-proteobacteria (6 to 18%). Out of a total 1,088 16S rRNA genes sequenced, 400 different operational taxonomic units were identified (>99.5% identity). Of these, 295 were novel (<99% identical to any sequences in the GenBank database). This study provides a comprehensive database for future examinations of changes in the bacterial community during bleaching events.

scholarly journals Bacterial Composition, Community Structure, and Diversity in Apis nigrocincta Gut

2020 ◽  
Vol 2020 ◽  
pp. 1-8 ◽  
Author(s):  
Christian Apolinaris Lombogia ◽  
Max Tulung ◽  
Jimmy Posangi ◽  
Trina Ekawati Tallei
Keyword(s):  
Community Structure ◽  
Illumina Miseq ◽  
Gut Bacteria ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bacterial Composition ◽  
Operational Taxonomic Units ◽  
Adult Worker ◽  
Gut Microbial Community ◽  
Apis Nigrocincta

Understanding the honeybee gut bacteria is an essential aspect as honeybees are the primary pollinators of many crops. In this study, the honeybee-associated gut bacteria were investigated by targeting the V3-V4 region of 16S rRNA genes using the Illumina MiSeq. The adult worker was captured in an urban area in a dense settlement. In total, 83,018 reads were obtained, revealing six phyla from 749 bacterial operational taxonomic units (OTUs). The gut was dominated by Proteobacteria (58% of the total reads, including Enterobacteriaceae 28.2%, Erwinia 6.43%, and Klebsiella 4.90%), Firmicutes (29% of the total reads, including Lactococcus garvieae 13.45%, Lactobacillus spp. 8.19%, and Enterococcus spp. 4.47%), and Actinobacteria (8% of the total reads, including Bifidobacterium spp. 7.96%). Many of these bacteria belong to the group of lactic acid bacteria (LAB), which was claimed to be composed of beneficial bacteria involved in maintaining a healthy host. The honeybee was identified as Apis nigrocincta based on an identity BLAST search of its COI region. This study is the first report on the gut microbial community structure and composition of A. nigrocincta from Indonesia.

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