A communal catalogue reveals Earth's multiscale microbial diversity

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.Peer reviewe

A communal catalogue reveals Earth’s multiscale microbial diversity

Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity

Application of innovative genomic and proteomic tools to medical entomology

Les maladies transmises par les arthropodes vecteurs sont responsables de centaines de milliers de cas d’infections humaines et de décès chaque année à travers le monde. Ces maladies, causées par des bactéries, virus ou parasites, parfois émergents ou réémergents, sont parfois peu connues ou sous-estimées. Les arthropodes peuvent être utilisés comme outil de suivi épidémiologique des micro-organismes qui leur sont associés et dont certains pourront être transmis à des hôtes vertébrés. L’identification des arthropodes reste cruciale dans les enquêtes entomologiques.Nous avons pu ainsi détecter de potentielles nouvelles bactéries dans les tiques de Tahiti et les triatomes de Guyane.Nous avons exploré le microbiote salivaire de près de mille moustiques de 3 pays différents par métagénomique 16S. Nous avons ainsi détecté un large nombre de bactéries pathogènes opportunistes mais aussi un très grand nombre de génotypes correspondant probablement à des espèces et genres bactériens nouveaux. Enfin notre axe majeur a été le développement de l’utilisation de la spectrométrie de masse MALDI-TOF en entomologie médicale. Pour pallier les limites des méthodes de référence d’identification des arthropodes existantes, nous avons validé l’utilisation de cet outil pour l’identification des moustiques (collectés sur terrain en Australie) et de puces (Espagne, Corse, Algérie). Nous avons également mis au point son utilisation pour l’identification de nouvelles familles d’arthropodes, comme les punaises de lits et les triatomes. Nous avons pu mettre en évidence, la capacité de la spectrométrie de masse MALDI-TOF pour différencier les anophèles infectés ou non par des plasmodies.Vector-borne diseases are responsible for hundreds of thousands of cases of human infections and deaths each year worldwide. Generally, little is known about these diseases, caused by bacteria, viruses or parasites, sometimes emerging or re-emerging. Arthropods can be used as a tool for epidemiological monitoring of their associated microorganisms, some of which being able to be transmitted to vertebrate hosts. The identification of arthropods remains crucial in entomological investigations.We were able to detect potential new bacteria in ticks from Tahiti and triatomines in French Guiana.We explored the salivary microbiota of nearly a thousand mosquitoes from 3 different countries by 16S rRNA metagenomics. We have thus detected a large number of opportunistic pathogenic bacteria but also a very large number of genotypes probably corresponding to new bacterial species and genera. Finally, our major focus has been the development of the use of MALDI-TOF mass spectrometry in medical entomology. To overcome the limitations of existing arthropod identification reference methods, we validated the use of this tool for the identification of mosquitoes (collected in the field in Australia) and fleas (Spain, Corsica, Algeria). We have also developed its use for the identification of new families of arthropods, such as bed bugs (Cimicidae) and triatomines (Reduviidae). We were able to highlight the capacity of MALDI-TOF mass spectrometry to differentiate between anopheles infected or not by malaria parasites

Detection of Bartonella spp. in Cimex lectularius by MALDI-TOF MS

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Use of MALDI-TOF MS for the Identification of Chad Mosquitoes and the Origin of Their Blood Meal

International audienceMatrix-assisted desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a clinical microbiology tool for the systematic identification of microorganisms. It has recently been presented as an innovative tool for the rapid and accurate identification of mosquitoes and their blood meal. To evaluate the capacity of this tool to identify mosquitoes collected in a tropical environment and preserved with silica gel, we analyzed 188 mosquitoes of different species collected in Chad, which were preserved with silica gel for 2 months. The MALDI-TOF MS analysis correctly identified 96% of the mosquitoes and 37.5% of their blood meals. Using MALDI-TOF MS and molecular biology, eight mosquito species were identified, including Anopheles gambiae s.l., Anopheles rufipes, Culex quinquefasciatus, Culex neavei, Culex pipiens, Culex perexiguus, Culex rima, and Culex watti. Blood meal identification revealed that mosquitoes fed mainly on humans, birds, and cows. Matrix-assisted desorption/ionization time-of-flight mass spectrometry appears to be a promising, fast, and reliable tool to identify mosquitoes and the origin of their blood meal for samples stored with silica gel

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry: an emerging tool for studying the vectors of human infectious diseases

International audienceArthropod vectors have historically been identified morphologically, and more recently using molecular biology methods. However, both of these methods are time-consuming and require specific expertise and equipment. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry, which has revolutionized the routine identification of microorganisms in clinical microbiology laboratories, was recently successfully applied to the identification of arthropod vectors. Since then, the robustness of this identification technique has been confirmed, extended to a large panel of arthropod vectors, and assessed for detecting blood feeding behavior and identifying the infection status in regard to certain pathogenic agents. In this study, we summarize the state-of-the-art of matrix-assisted laser desorption ionization time-of-flight mass spectrometry applied to the identification of arthropod vectors (ticks, mosquitoes, phlebotomine sand-flies, fleas, triatomines, lice and Culicoides), their trophic preferences and their ability to discriminate between infection statuses

Tick- and flea-borne rickettsioses in Tizi-Ouzou, Algeria: Implications for travel medicine

International audienceBackground: In Algeria, Mediterranean spotted fever (MSF), caused by Rickettsia conorii conorii and transmitted by Rhipicephalus sanguineus, is endemic. However, the documentation of cases is rare due to a lack of laboratory facilities. Our aim was to screen for rickettsioses in patients with fever, rash and a possible inoculation eschar. Materials and methods: Between 2013 and 2015, patients with a fever and a rash presenting at hospitals in the Tizi-Ouzou region were prospectively included in our study. Sera were screened using Indirect Immunofluorescence Assay (IFA) and qPCR was performed on swab samples from eschars. Results: One hundred and sixty-six patients were included. For 57 patients, MSF due to R. conorii conorii was diagnosed by serology and qPCR on a swab eschar sample. Three patients were diagnosed with murine typhus, a flea borne rickettsiosis. In addition, two patients had a positive serology in IgM for R. felis. For nine patients, serology for rickettsiosis was positive, but the specific rickettsia involved could not be determined. Nine patients had a severe disease with neurological involvement or multi-organ failure. Conclusion: Clinicians should routinely screen for rickettsioses in patients and travellers presenting with a rash upon return from Algeria. Doxycycline treatment must be given promptly because the prognosis can be severe

Blood meal identification in the cryptic species Anopheles gambiae and Anopheles coluzzii using MALDI-TOF MS

International audienceMatrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has recently emerged in entomology as a technique to identify arthropods and their blood meal source. In this study, female Anopheles gambiae were fed on five host blood sources: ocelot (Leopardus pardalis), binturong (Arctictis binturong), springbok (Antidorcas marsupialis), jaguar (Panthera onca) and Hamadryas baboon (Papio hamadryas), while Anopheles coluzzii were fed on three hosts: dromedary (Camelus dromedarius), Barbary sheep (Ammotragus lervia) and pig (Sus scrofa). We obtained the MS spectra from 240 engorged mosquito abdomens and selected high quality ones from 72 mosquito abdomens to upgrade our home-made database. We excluded from the analysis any spectra of low quality (n = 80), and the remaining 88 specimens were subjected to a blind test analysis against the home-made database. We obtained 100% correct identification of the blood meal source for the specimens collected, 1, 12 and 24 h post-feeding, whereas for the specimens collected 36 h post-feeding, the correct identification rate decreased dramatically. We confirm here that MALDI-TOF MS can be used to identify the blood meal origin of freshly engorged mosquitoes, which opens new perspectives for further studies, including the impact of the mosquito species on blood meal identification

Agents zoonotiques vectorisés étudiés à l’Institut Hospitalo-Universitaire Méditerranée Infection

Zoonotic vector-borne diseases at the university hospital institute mediterranee infection. Medical entomology is dedicated to the study of arthropods that are involved with human health but also animal health as many zoonotic diseases have been emerging all around the world for the past few years. We hereby introduce some research fields developed by the Medical Entomology team of the University Hospital Institute Méditerranée Infection, illustrated with recent or emblematic studies : technical innovation for identification of arthropods, the use of arthropods as epidemiological or diagnostic tool, entomological investigations around clinical cases and the development of experimental models for a better understanding of interactions between arthropods, humans and microorganisms.L’entomologie médicale est l’étude des arthropodes vecteurs d’agents pathogènes responsables de maladies humaines, dont de nombreuses zoonoses émergentes ces dernières années. Nous présentons ici quelques axes de recherche développés par l’équipe d’Entomologie Médicale de l’Institut Hospitalo-Universitaire Méditerranée Infection, illustrés par des études récentes ou emblématiques : l’innovation technologique pour identifier les arthropodes, l’utilisation des arthropodes comme outil épidémiologique ou diagnostique, les enquêtes autour de cas cliniques et les modèles expérimentaux pour comprendre les interactions entre les arthropodes, l’homme et les microorganismes. RésuméLaroche Maureen, Alméras Lionel, Bérenger Jean-Michel, Raoult Didier, Parola Philippe. Agents zoonotiques vectorisés étudiés à l’Institut Hospitalo-Universitaire Méditerranée Infection. In: Bulletin de l'Académie Vétérinaire de France tome 168 n°3, 2015. pp. 245-252