Microbiota identified from preserved Anopheles

Abstract Background Mosquito species from the Anopheles gambiae complex and the Anopheles funestus group are dominant African malaria vectors. Mosquito microbiota play vital roles in physiology and vector competence. Recent research has focused on investigating the mosquito microbiota, especially in wild populations. Wild mosquitoes are preserved and transported to a laboratory for analyses. Thus far, microbial characterization post-preservation has been investigated in only Aedes vexans and Culex pipiens. Investigating the efficacy of cost-effective preservatives has also been limited to AllProtect reagent, ethanol and nucleic acid preservation buffer. This study characterized the microbiota of African Anopheles vectors: Anopheles arabiensis (member of the An. gambiae complex) and An. funestus (member of the An. funestus group), preserved on silica desiccant and RNAlater® solution. Methods Microbial composition and diversity were characterized using culture-dependent (midgut dissections, culturomics, MALDI-TOF MS) and culture-independent techniques (abdominal dissections, DNA extraction, next-generation sequencing) from laboratory (colonized) and field-collected mosquitoes. Colonized mosquitoes were either fresh (non-preserved) or preserved for 4 and 12 weeks on silica or in RNAlater®. Microbiota were also characterized from field-collected An. arabiensis preserved on silica for 8, 12 and 16 weeks. Results Elizabethkingia anophelis and Serratia oryzae were common between both vector species, while Enterobacter cloacae and Staphylococcus epidermidis were specific to females and males, respectively. Microbial diversity was not influenced by sex, condition (fresh or preserved), preservative, or preservation time-period; however, the type of bacterial identification technique affected all microbial diversity indices. Conclusions This study broadly characterized the microbiota of An. arabiensis and An. funestus. Silica- and RNAlater®-preservation were appropriate when paired with culture-dependent and culture-independent techniques, respectively. These results broaden the selection of cost-effective methods available for handling vector samples for downstream microbial analyses.

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The Potential of a Polyphasic PCR-DGGEApproach in Evaluating Microbial Diversity of Natural Whey Cultures for Water-Buffalo Mozzarella Cheese Production: Bias of Culture-Dependent and Culture-Independent Analyses

Systematic and Applied Microbiology ◽

10.1078/0723-2020-00076 ◽

2001 ◽

Vol 24 (4) ◽

pp. 610-617 ◽

Cited By ~ 145

Author(s):

Danilo Ercolini ◽

Giancarlo Moschetti ◽

Giuseppe Blaiotta ◽

Salvatore Coppola

Keyword(s):

Microbial Diversity ◽

Water Buffalo ◽

Mozzarella Cheese ◽

Culture Independent ◽

Cheese Production ◽

Culture Dependent

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Microbial Diversity Associated with Gwell, a Traditional French Mesophilic Fermented Milk Inoculated with a Natural Starter

Microorganisms ◽

10.3390/microorganisms8070982 ◽

2020 ◽

Vol 8 (7) ◽

pp. 982

Author(s):

Lucas von Gastrow ◽

Marie-Noëlle Madec ◽

Victoria Chuat ◽

Stanislas Lubac ◽

Clémence Morinière ◽

...

Keyword(s):

Microbial Community ◽

Fermentation Process ◽

Fermented Milk ◽

Geotrichum Candidum ◽

Microbial Composition ◽

Streptococcus Species ◽

Culture Independent ◽

History Of ◽

Points Of View ◽

Culture Dependent

Gwell is a traditional mesophilic fermented milk from the Brittany region of France. The fermentation process is based on a back-slopping method. The starter is made from a portion of the previous Gwell production, so that Gwell is both the starter and final product for consumption. In a participatory research framework involving 13 producers, Gwell was characterized from both the sensory and microbial points of view and was defined by its tangy taste and smooth and dense texture. The microbial community of typical Gwell samples was studied using both culture-dependent and culture-independent approaches. Lactococcus lactis was systematically identified in Gwell, being represented by both subspecies cremoris and lactis biovar diacetylactis which were always associated. Geotrichum candidum was also found in all the samples. The microbial composition was confirmed by 16S and ITS2 metabarcoding analysis. We were able to reconstruct the history of Gwell exchanges between producers, and thus obtained the genealogy of the samples we analyzed. The samples clustered in two groups which were also differentiated by their microbial composition, and notably by the presence or absence of yeasts identified as Kazachstania servazii and Streptococcus species.

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Assessment of Microbial Diversity in Saudi Springs by Culture-Dependent and Culture-Independent Methods

Geomicrobiology Journal ◽

10.1080/01490451.2016.1219430 ◽

2016 ◽

pp. 1-11

Author(s):

Samy Selim ◽

Sherif Hassan ◽

Nashwa Hagagy ◽

Lucia Kraková ◽

Tomaš Grivalský ◽

...

Keyword(s):

Microbial Diversity ◽

Culture Independent ◽

Culture Dependent

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Rapid ageing and species identification of natural mosquitoes for malaria surveillance

10.1101/2020.06.11.144253 ◽

2020 ◽

Author(s):

Doreen J. Siria ◽

Roger Sanou ◽

Joshua Mitton ◽

Emmanuel P. Mwanga ◽

Abdoulaye Niang ◽

...

Keyword(s):

Mosquito Species ◽

Natural Populations ◽

Cost Effective ◽

Malaria Vectors ◽

Sampling Effort ◽

Malaria Surveillance ◽

Vector Borne Diseases ◽

Vector Borne ◽

Species Specific ◽

The Impact

AbstractThe malaria parasite, which is transmitted by several Anopheles mosquito species, requires more time to reach its human-transmissible stage than the average lifespan of a mosquito. Monitoring the species-specific age structure of mosquito populations is critical to evaluating the impact of vector control interventions on malaria risk. We developed a rapid, cost-effective surveillance method based on deep learning of mid-infrared spectra of mosquitoes’ cuticle that simultaneously identifies the species and the age of three main malaria vectors, in natural populations. Using over 40,000 ecologically and genetically diverse females, we could speciate and age grade An. gambiae, An. arabiensis, and An. coluzzii with up to 95% accuracy. Further, our model learned the age of new populations with minimal sampling effort and detected the impact of control interventions on simulated mosquito populations, measured as a shift in their age structures. We anticipate our method to be applied to other arthropod vector-borne diseases.

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Detection and phylogenetic analysis of coastal bioaerosols using culture dependent and independent techniques

Biogeosciences ◽

10.5194/bg-8-301-2011 ◽

2011 ◽

Vol 8 (2) ◽

pp. 301-309 ◽

Cited By ~ 44

Author(s):

R. Urbano ◽

B. Palenik ◽

C. J. Gaston ◽

K. A. Prather

Keyword(s):

Atmospheric Chemistry ◽

Cloud Droplet ◽

Independent Study ◽

Rrna Gene ◽

Monitoring Site ◽

Microbial Composition ◽

Atmospheric Processes ◽

Erosion Processes ◽

Culture Independent ◽

Culture Dependent

Abstract. Bioaerosols are emerging as important yet poorly understood players in atmospheric processes. Microorganisms can impact atmospheric chemistry through metabolic reactions and can potentially influence physical processes by participating in ice nucleation and cloud droplet formation. Microbial roles in atmospheric processes are thought to be species-specific and potentially dependent on cell viability. Using a coastal pier monitoring site as a sampling platform, culture-dependent (i.e. agar plates) and culture-independent (i.e. DNA clone libraries from filters) approaches were combined with 18S rRNA and 16S rRNA gene targeting to obtain insight into the local atmospheric microbial composition. From 13 microbial isolates and 42 DNA library clones, a total of 55 sequences were obtained representing four independent sampling events. Sequence analysis revealed that in these coastal samples two fungal phyla, Ascomycota and Basidiomycota, predominate among eukaryotes while Firmicutes and Proteobacteria predominate among bacteria. Furthermore, our culture-dependent study verifies the viability of microbes from all four phyla detected through our culture-independent study. Contrary to our expectations and despite oceanic air mass sources, common marine planktonic bacteria and phytoplankton were not typically found. The abundance of terrestrial and marine sediment-associated microorganisms suggests a potential importance for bioaerosols derived from beaches and/or coastal erosion processes.

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Molecular Identification of Bacteria in Intra-abdominal Abscesses Using Deep Sequencing

Open Forum Infectious Diseases ◽

10.1093/ofid/ofy025 ◽

2018 ◽

Vol 5 (2) ◽

Cited By ~ 5

Author(s):

Andrew Kozlov ◽

Lorenzo Bean ◽

Emilie V Hill ◽

Lisa Zhao ◽

Eric Li ◽

...

Keyword(s):

16S Rrna ◽

Microbial Diversity ◽

Diversity Index ◽

Disease Process ◽

Microbial Composition ◽

Bacterial Consortia ◽

Abdominal Abscesses ◽

Culture Independent ◽

Standard Culture ◽

Culture Negative

Abstract Background Intra-abdominal abscesses are localized collections of pus, which generally arise from a breach in the normal mucosal defense barrier that allows bacteria from gastrointestinal tract, and less commonly from the gynecologic or urinary tract, to induce inflammation, resulting in an infection. The microbiology of these abscesses is usually polymicrobial, associated with the primary disease process. However, the microbial identity, diversity and richness in intra-abdominal abscesses have not been well characterized, due in part to the difficulty in cultivating commensal organisms using standard culture-based techniques. Methods We used culture-independent 16S rRNA Illumina sequencing to characterize bacterial communities in intra-abdominal abscesses collected by percutaneous drainage. A total of 43 abscess samples, including 19 (44.2%) Gram stain and culture-negative specimens, were analyzed and compared with results from conventional microbiologic cultures. Results Microbial composition was determined in 8 of 19 culture-negative samples and 18 of 24 culture-positive samples, identifying a total of 221 bacterial taxa or operational taxonomic units (OTUs) and averaging 13.1 OTUs per sample (interquartile range, 8–16.5 OTUs). Microbial richness for monomicrobial and polymicrobial samples was significantly higher than culture-negative samples (17 and 15.2 OTUs vs 8 OTUs, respectively), with a trend toward a higher microbial diversity (Shannon diversity index of 0.87 and 1.18 vs 0.58, respectively). Conclusions The bacterial consortia identified by cultures correlated poorly with the microbial composition determined by 16S rRNA sequencing, and in most cases, the cultured isolates were minority constituents of the overall abscess microbiome. Intra-abdominal abscesses were generally polymicrobial with a surprisingly high microbial diversity, but standard culture-based techniques failed to reveal this diversity. These data suggest that molecular-based approaches may be helpful for documenting the presence of bacteria in intra-abdominal abscesses where standard cultures are unrevealing, particularly in the setting of prior antibiotic exposure.

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