Temporal patterns in Ixodes ricinus microbial communities: an insight into tick-borne microbe interactions.

BACKGROUND: Ticks transmit pathogens of medical and veterinary importance and are an increasing threat to human and animal health. Assessing disease risk and developing new control strategies requires identifying members of the tick-borne microbiota as well as their temporal dynamics and interactions. METHODS: Using high-throughput sequencing, we studied the Ixodes ricinus microbiota and its temporal dynamics. 371 nymphs were monthly collected during three consecutive years in a peri-urban forest. After a Poisson lognormal model was adjusted to our data set, a principal component analysis, sparse network reconstruction, and differential analysis allowed us to assess seasonal and monthly variability of I. ricinus microbiota and interactions within this community. RESULTS: Around 75% of the detected sequences belonged to five genera known to be maternally inherited bacteria in arthropods and to potentially circulate in ticks: Candidatus Midichloria, Rickettsia, Spiroplasma, Arsenophonus and Wolbachia. The structure of the I. ricinus microbiota varied over time with interannual recurrence and seemed to be mainly driven by OTUs commonly found in the environment. Total network analysis revealed a majority of positive partial correlations. We identified strong relationships between OTUs belonging to Wolbachia and Arsenophonus, evidence for the presence of the parasitoid wasp Ixodiphagus hookeri in ticks. Other associations were observed between the tick symbiont Candidatus Midichloria and pathogens belonging to Rickettsia. Finally, more specific network analyses were performed on TBP-infected samples and suggested that the presence of pathogens belonging to the genera Borrelia, Anaplasma and Rickettsia may disrupt microbial interactions in I. ricinus. CONCLUSIONS: We identified the I. ricinus microbiota and documented marked shifts in tick microbiota dynamics over time. Statistically, we showed strong relationships between the presence of specific pathogens and the structure of the I. ricinus microbiota. We detected close links between some tick symbionts and the potential presence of either pathogenic Rickettsia or a parasitoid in ticks. These new findings pave the way for the development of new strategies for the control of ticks and tick-borne diseases. Video abstract.

Diversity and dynamics of bacterial and fungal communities in cider for distillation.

Bacterial and fungal population dynamics in cider for distillation have so far been explored by culture-dependant methods. Cider for distillation can be produced by the spontaneous fermentation of apples that do not undergo any intervention during the process. In this study, cider microbiomes extracted from six tanks containing ciders for distillation from four producers in Normandy were characterized at three main stages of the fermentation process: fermentation Initiation (I), end of the alcoholic Fermentation (F) and end of the Maturation period (M). Cider samples were subjected to Illumina MiSeq sequencing (rRNA 16S V1-V3 and ITS1 region targeting) to determine bacterial and fungal communities. Yeasts (YGC), Zymomonas (mZPP) and lactic acid bacteria selective media (mMRS, mMLO, mPSM) were also used to collect 807 isolates. Alcoholic levels, glycerol, sugar content (glucose, fructose and sucrose), pH, total and volatile acidity, nitrogen, malic and lactic acid contents were determined at all sampling points. Alpha diversity indexes show significant differences (p < 0.05) in microbial populations between I, F and M. Fungal communities were characterized by microorganisms from the environment and phytopathogens at I followed by the association of yearsts with alcoholic fermentation like Saccharomyces and non-Saccharomyces yeasts (Hanseniaspora, Candida). A maturation period for cider leads to an increase of the Dekkera/Brettanomyces population, which is responsible for off-flavors in cider for all producers. Among bacterial communities, the genera community associated to malolactic fermentation (Lactobacillus sp., Leuconostoc sp., Oenococcus sp.) was the most abundant at F and M. Acetic acid bacteria such as Acetobacter sp., Komagataeibacter sp. and Gluconobacter sp. were also detected during the process. Significant differences (p < 0.05) were found in fungal and bacterial populations between the four producers and during the fermentation process. The development of microorganisms associated with cider spoilage such as Zymomonas mobilis, Lactobacillus collinoides or Brettanomyces/Dekkera sp. was anticipated by a metagenomic approach. The monitoring of microbial diversity via high throughput sequencing combined with physical-chemical analysis is an interesting approach to improve the fermentation performance of cider for distillation and therefore, the quality of Calvados.

Assessing the quality of fresh Whitemouth croaker (Micropogonias furnieri) meat based on micro-organism and histamine analysis using NGS, qPCR and HPLC-DAD.

AIMS: Quality evaluation of fresh whitemouth croaker (Micropogonias furnieri) by histamine determination using the HPLC-DAD method and quantification of histamine-forming bacteria using NGS and qPCR. METHODS AND RESULTS: The histamine content of fresh whitemouth croaker was detected by high performance liquid chromatography with diode array detector with a concentration ranging from 258·52 to 604·62 mg kg-1 being observed. The number of histidine decarboxylase (hdc gene) copies from Gram-negative bacteria and the bacteria Morganella morganii and Enterobacter aerogenes were quantified by quantitative polymerase chain reaction. All samples were positive, with copy numbers of the hdc gene ranging from 4·67 to 12·01 log10 per g. The microbial community was determined by sequencing the V4 region of the 16S rRNA gene using the Ion Torrent platform. The bioinformatics data generated by frog software showed that the phylum Proteobacteria was the most abundant, with the family Moraxellaceae being more prevalent in samples collected in the summer, whereas the Pseudomonadaceae was more present in the winter. CONCLUSIONS: All fish muscle samples analysed in this study presented histamine values higher than those allowed by CODEX Alimentarius. Additionally, a wide variety of spoilage micro-organisms capable of expressing the enzyme histidine decarboxylase were detected. Thus, improvements in handling and processing are required to minimize the prevalence of histamine-producing bacteria in fish. SIGNIFICANCE AND IMPACT OF THE STUDY: Global fish production in 2016 was 171 million tons, with the largest consumer being China, followed by Indonesia and the USA. In Brazil, 1·3 million tons of fish are consumed per year, with whitemouth croaker being the main fish landed. Notably, cases associated with histamine poisoning are quite common. According to the European Food Safety Authority and European Centre for Disease Prevention and Control, a total of 599 HFP outbreaks were identified in the European Union during the period 2010-2017. In the USA, there were 333 outbreaks with 1383 people involved between 1998 and 2008.

Characterization of the mechanical behaviour parameters of the costo-vertebral joint.

This in vitro study introduces a new method to determine quantitative parameters characterizing the mechanical behaviour of the costo-vertebral joint. These parameters are useful in building numerical models of the thoracic spine, taking into account the thoracic cage. Nine thoracic cages were isolated from fresh human cadavers. From each cage, three functional units were tested: T1-T2, T5-T6, T9-T10. Loads were applied according to the joint local coordinate system. Every functional unit was tested first intact and again after section of successive costo-transverse ligaments. We used an opto-electronic system to follow the three-dimensional motion of the joint, and obtained non-linear load/displacement curves according to the primary rotation axis. A statistical analysis of these curves allowed the calculation of parameters describing the joint mechanical behaviour: total range of motion, motion in the low-stiffness zone, and flexibilities in the positive and negative quasi-linear zones. These values can be used as a database for mechanical modeling of the spine.