Biology subjects

Flandrois, J.-P.

Publications and source records attributed to Flandrois, J.-P..

5 recordsLinked to original sources

bioRxiv2024

High δ15N values in Predynastic Egyptian archeological remains: A potential indicator for localised soil fertilisation practices in extreme conditions

Predynastic Egypt arose around 5700 BC when nomadic people settled in the Nile Valley. Without voluntary practice related to anthropic mummification, as will be seen with the Egyptian Dynastic empires, human remains from this period were naturally mummified because of the natural environmental conditions, possibly enveloped in plant mats and animal skins. This study focuses on four mummies from the Natural History Museum of Musee des Confluences in Lyon (France). The geographic origin of the mummies and climatic conditions at that time were deduced from o18O measurements on teeth and bones. These measurements confirm that the primary source of drinking water was the Nile, and that one mummy of unknown origin also originated from Upper Egypt like the other three. The diet and life habits of these individuals were inferred from carbon (o13C), nitrogen (o15N) and sulfur (o34S) isotope compositions of their skins and bone collagens. Our study is of particular interest as we were able to analyse the animal skins and plant material enveloping the mummies using the same isotopic systems. The mean o15N values obtained in human skins (17.9{+/-}2.4{per thousand}, AIR) were found to be high, and consistent with the values measured in animal skins (16.0{+/-}2.9{per thousand}, AIR). The analysed plants have even higher values, with an average of 22.1{+/-}2.2{per thousand}, AIR. The most probable explanation for the markedly elevated {delta}15N values observed in all the materials investigated is localised soil amendment practices. This is corroborated by the consistent nitrogen isotopic signatures across all the examined tissues, with a notable prevalence in plant tissues.

ecology↗

bioRxiv2023

Description of a new genus of the Pectobacteriaceae family isolated from lake water in France; Prodigiosinella aquatilis gen. nov. sp. nov. includes two subspecies Prodigiosinella aquatilis subsp. aquatilis ssp. nov. and Prodigiosinella aquatilis subsp. natabilis ssp. nov.

The Pectobacteriaceae family comprises plant pathogens able to provoke diverse diseases, including plant maceration due to the production of pectinases disrupting the plant cell wall. To better understand their natural diversity, a survey of pectinolytic bacteria was performed in lakes of the French region La Camargue near the Mediterranean Sea. Sixteen atypical pectinolytic isolates were obtained from brackish water of three lakes. The genome of six isolates was sequenced; their size is around 4.8 to 5.0 Mb, including a plasmid of 59 to 61 kb; their G+C values range from 49.1 to 49.3 mol%. Phylogenetic analyses indicated that the novel strains formed a new clade of Pectobacteriaceae, separate from previously described genera of this family. These analyses suggested also that Acerihabitans does not belong to Pectobacteriaceae and should be reclassified in the Bruguierivoracaceae family, while Symbiopectobacterium could be a true Pectobacteriaceae member. Based on phenotypic, genomic and phylogenetic characteristics, we propose the creation of a new genus with the name Prodigiosinella gen. nov. Both the phenotypic and phylogenetic analyses separated the strains into two distinct subgroups. However, the DNA-DNA relatedness values revealed a close relationship between the two groups, supporting their appurtenance to the same species. Thus, it is proposed to classify them as two subspecies of Prodigiosinella aquatilis sp. nov., for which we propose the name Prodigiosinella aquatilis subsp. aquatilis ssp. nov. (LS101T = CFBP 8826T = LMG 32072T) and Prodigiosinella aquatilis subsp. natabilis ssp. nov. (CE70T = CFBP 9054T = LMG 32867T).

microbiology↗

bioRxiv2019

Metapopulation ecology links antibiotic resistance, consumption and patient transfers in a network of hospital wards

Antimicrobial resistance (AMR) is a global threat. A better understanding of how antibiotic use and between ward patient transfers (or connectivity) impact hospital AMR can help optimize antibiotic stewardship and infection control strategies. Here, we used metapopulation ecology to explain variations in infection incidences of 17 ESKAPE pathogen variants in a network of 357 hospital wards. Multivariate models identified the strongest influence of ward-level antibiotic use on more resistant variants, and of connectivity on nosocomial species and carbapenem-resistant variants. Pairwise associations between infection incidence and the consumption of specific antibiotics were significantly stronger when such associations represented a priori AMR selection, suggesting that AMR evolves within the network. Piperacillin-tazobactam consumption was the strongest predictor of the cumulative incidence of infections resistant to empirical sepsis therapy. Our data establish that both antibiotic use and connectivity measurably influence hospital AMR and provide a ranking of key antibiotics by their impact on AMR.

ecology↗

bioRxiv2019

A sample-to-report solution for taxonomic identification of cultured bacteria in the clinical setting based on nanopore sequencing

Amplicon sequencing of 16S rRNA gene is commonly used for the identification of bacterial isolates in diagnostic laboratories, and mostly relies on the Sanger sequencing method. The latter, however, suffers from a number of limitations with the most significant being the inability to resolve mixed amplicons when closely related species are co-amplified from a mixed culture. This often leads to either increased turnover time or absence of usable sequence data. Short-read NGS technologies could address the mixed amplicon issue, but would lack both cost efficiency at low throughput and fast turnaround times. Nanopore sequencing developed by Oxford Nanopore Technologies (ONT) could solve those issues by enabling flexible number of samples per run and adjustable sequencing time. Here we report on the development of a standardized laboratory workflow combined with a fully automated analysis pipeline LORCAN (Long Read Consensus ANalysis), which together provide a sample-to-report solution for amplicon sequencing and taxonomic identification of the resulting consensus sequences. Validation of the approach was conducted on a panel of reference strains and on clinical samples consisting of single or mixed rRNA amplicons associated with various bacterial genera by direct comparison to the corresponding Sanger sequences. Additionally, artificial read mixtures of closely related species were used to assess LORCANs behaviour when dealing with samples with known cross-contamination level. We demonstrate that by combining ONT amplicon sequencing results with LORCAN, the accuracy of Sanger sequencing can be closely matched (>99.6% sequence identity) and that mixed samples can be resolved at the single base resolution level. The presented approach has the potential to significantly improve the flexibility, reliability and availability of amplicon sequencing in diagnostic settings.

microbiology↗

bioRxiv2019

The phytopathogenic nature of Dickeya aquatica 174/2 and the dynamic early evolution of Dickeya pathogenicity

Originality-Significance statementAlthough the reach of large-scale comparative studies has spread exponentially over the years, the phytopathogenic Dickeya group remains overlooked. In this work, we sequence the complete genome of Dickeya aquatica type strain, a species isolated from water that was first assumed to be non-phytopathogenic. We show that the proteome of D. aquatica contains a wide number of proteins involved in Dickeya virulence, including plant cell wall degrading enzymes, suggesting that this species could be in fact pathogenic. Using experimental approaches, we confirm this prediction and uncover the particular affinity of D. aquatica for acidic fruits. In-depth phylogenomic analyses reveal that Dickeya species display a great degree of genetic plasticity in the pathogenicity determinants, explaining how this bacterial group was able to colonize a wide variety of plants growing in different climates. These observations greatly advance our understanding of how bacteria adapt to new ecological niches.\n\nSummaryDickeya is a genus of phytopathogenic enterobacterales causing soft rot in a variety of plants (e.g. potato, chicory, maize). Among the species affiliated to this genus, Dickeya aquatica, described in 2014, remained particularly mysterious because it had no known host. Furthermore, while D. aquatica was proposed to represent a deep-branching species among Dickeya genus, its precise phylogenetic position remained elusive.\n\nHere, we report the complete genome sequence of the D. aquatica type strain 174/2. We demonstrate the affinity of D. aquaticaT for acidic fruits such as tomato and cucumber, and show that exposure of this bacterium to acidic pH induces twitching motility. An in-depth phylogenomic analysis of all available Dickeya proteomes pinpoints D. aquatica as the second deepest branching lineage within this genus and reclassifies two lineages that likely correspond to new genomospecies (gs.): Dickeya gs. poaceaephila (Dickeya sp NCPPB 569) and Dickeya gs. undicola (Dickeya sp 2B12), together with a new putative genus, tentatively named Prodigiosinella. Finally, from comparative analyses of Dickeya proteomes we infer the complex evolutionary history of this genus, paving the way to study the adaptive patterns and processes of Dickeya to different environmental niches and hosts. In particular, we hypothetize that the lack of xylanases and xylose degradation pathways in D. aquatica could reflects adaptation to aquatic charophyte hosts which, in contrast to land plants, do not contain xyloglucans.

genomics↗