The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Insect heritable symbionts have proven to be ubiquitous, based on molecular screening of various insect lineages. Recently, molecular and experimental approaches have yielded an immensely richer understanding of their diverse biological roles, resulting in a burgeoning research literature. Increasingly, commonalities and intermediates are being discovered between categories of symbionts once considered distinct: obligate mutualists that provision nutrients, facultative mutualists that provide protection against enemies or stress, and symbionts such as Wolbachia that manipulate reproductive systems. Among the most farreaching impacts of widespread heritable symbiosis is that it may promote speciation by increasing reproductive and ecological isolation of host populations, and it effectively provides a means for transfer of genetic information among host lineages. In addition, insect symbionts provide some of the extremes of cellular genomes, including the smallest and the fastest evolving, raising new questions about the limits of evolution of life.

Genomics and Evolution of Heritable Bacterial Symbionts

The most recent version of the OIE Manual of Diagnostic Tests and Vaccines for Terrestrial Animals (the Terrestrial Manual) is online: http://www.oie.int/en/international...

OIE Manual of Diagnostic Tests and Vaccines for Terrestrial Animals

https://onlinelibrary.wiley.com/doi/pdf/10.1111/1469-0691.12023

Microbial culturomics: paradigm shift in the human gut microbiome study

https://www.cell.com/trends/biotechnology/pdf/S0167-7799(13)00030-9.pdf

Antibacterial surfaces: the quest for a new generation of biomaterials.

A biofilm can be defined as a community of microorganisms adhering to a surface and surrounded by a complex matrix of extrapolymeric substances. It is now generally accepted that the biofilm growth mode induces microbial resistance to disinfection that can lead to substantial economic and health concerns. Although the precise origin of such resistance remains unclear, different studies have shown that it is a multifactorial process involving the spatial organization of the biofilm. This review will discuss the mechanisms identified as playing a role in biofilm resistance to disinfectants, as well as novel anti-biofilm strategies that have recently been explored.

https://www.tandfonline.com/doi/pdf/10.1080/08927014.2011.626899

Resistance of bacterial biofilms to disinfectants: a review

Free-living amoebae (FLA) are ubiquitous organisms that have been isolated from various domestic water systems, such as cooling towers and hospital water networks. In addition to their own pathogenicity, FLA can also act as Trojan horses and be naturally infected with amoeba-resisting bacteria (ARB) that may be involved in human infections, such as pneumonia. We investigated the biodiversity of bacteria and their amoebal hosts in a hospital water network. Using amoebal enrichment on nonnutrient agar, we isolated 15 protist strains from 200 (7.5%) samples. One thermotolerant Hartmannella vermiformis isolate harbored both Legionella pneumophila and Bradyrhizobium japonicum. By using amoebal coculture with axenic Acanthamoeba castellanii as the cellular background, we recovered at least one ARB from 45.5% of the samples. Four new ARB isolates were recovered by culture, and one of these isolates was widely present in the water network. Alphaproteobacteria (such as Rhodoplanes, Methylobacterium, Bradyrhizobium, Afipia, and Bosea) were recovered from 30.5% of the samples, mycobacteria (Mycobacterium gordonae, Mycobacterium kansasii, and Mycobacterium xenopi) were recovered from 20.5% of the samples, and Gammaproteobacteria (Legionella) were recovered from 5.5% of the samples. No Chlamydia or Chlamydia-like organisms were recovered by amoebal coculture or detected by PCR. The observed strong association between the presence of amoebae and the presence of Legionella (P < 0.001) and mycobacteria (P = 0.009) further suggests that FLA are a reservoir for these ARB and underlines the importance of considering amoebae when water control measures are designed.

Biodiversity of amoebae and amoeba-resisting bacteria in a hospital water network.

An increasing number of microorganisms, including bacteria but also viruses and eukaryotes, have been described as benefiting from interaction with free-living amoebae (FLA). Beneficial interaction can be due to resistance to predation conferring ecological advantage, intracellular survival and/or intracellular proliferation. This review highlights the potential risk associated with amoebae by listing all known pathogenic microbial species for which growth and/or survival promotion by FLA (mainly Acanthamoeba spp.) has been demonstrated. It focuses on the susceptibility of amoebal and intra-amoebal bacteria to various categories of biocides, the known mechanisms of action of these biocides against trophozoites and cysts and the various methods used to demonstrate efficacy of treatments against FLA. Brief descriptions of FLA ecology and prevalence in domestic/institutional water systems and their intrinsic pathogenicity are also presented. The intention is to provide an informed opinion on the environmental risks associated with the presence of FLA and on the survival of cysts following biocidal treatments, while also highlighting the need to conduct research on the roles of amoebae in aquatic ecosystems.

Free-living amoebae and their intracellular pathogenic microorganisms: risks for water quality.

Summary
The complex ecology of free-living amoebae (FLA) and their role in spreading pathogenic microorganisms through water systems have recently raised considerable interest. In this study, we investigated the presence of FLA and amoebae-resisting bacteria (ARB) at various stages of a drinking water plant fed with river water. We isolated various amoebal species from the river and from several points within the plant, mostly at early steps of water treatment. Echinamoeba- and Hartmannella-related amoebae were mainly recovered in the drinking water plant whereas Acanthamoeba- and Naegleria-related amoebae were recovered from the river water and the sand filtration units. Some FLA isolates were recovered immediately after the ozonation step, thus suggesting resistance of these microorganisms to this disinfection procedure. A bacterial isolate related to Mycobacterium mucogenicum was recovered from an Echinamoeba-related amoeba isolated from ozone-treated water. Various other ARB were recovered using co-culture with axenic Acanthamoeba castellanii, including mycobacteria, legionella, Chlamydia-like organisms and various proteobacteria. Noteworthy, a new Parachlamydia acanthamoebae strain was recovered from river water and from granular activated carbon (GAC) biofilm. As amoebae mainly multiply in sand and GAC filters, optimization of filter backwash procedures probably offers a possibility to better control these protists and the risk associated with their intracellular hosts.

Biodiversity of amoebae and amoebae-resisting bacteria in a drinking water treatment plant.

Aims: Monitoring of microbial changes during and after application of various disinfection treatments in a model domestic water system



Methods and Results:  A pilot-scale domestic water system consisting of seven galvanized steel re-circulation loops and copper dead legs was constructed Culture techniques, confocal laser scanning microscopy after fluorescent in situ hybridization and viability staining with the BacLight® LIVE/DEAD kit were used for planktonic and biofilm flora monitoring Before starting the treatments, the system was highly contaminated with Legionella pneumophila and biofilm populations mainly consisted of β-proteobacteria In the water and the biofilm of the loops, continuous application of chlorine dioxide (0·5 mg l−1), or chlorine (2·5 mg l−1) were very effective in reducing the microbial flora, including L pneumophila Heterotrophic bacteria, although strongly reduced, were still detectable after ozone application (0·5 mg l−1), whereas with monochloramine (0·5 mg l−1) and copper–silver ionization (0·8/0·02 mg l−1), the contamination remained significantly higher Monochloramine and copper–silver did not remove the biofilm During copper–silver application, Legionella re-growth was observed Only chlorine dioxide led to detectable effects in the dead leg Amoebae could not be eliminated, and after interrupting the treatments, L pneumophila quickly recovered their initial levels, in all cases



Conclusions:  Chlorine dioxide, applied as a continuous treatment, was identified in this study as the most efficient for controlling L pneumophila in a domestic water system Chlorine dioxide showed a longer residual activity, leading to improved performance in the dead leg Amoebae resisted to all the treatments applied and probably acted as reservoirs for L pneumophila, allowing a quick re-colonization of the system once the treatments were interrupted



Significance and Impact of the Study:  Control of microbial contamination requires maintenance of a constant disinfectant residual throughout the water system Treatment strategies targeting free-living amoebae should lead to improved control of L pneumophila Such treatment strategies still have to be investigated

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-2672.2004.02391.x

Vincent Thomas

Papers

Resistance of bacterial biofilms to disinfectants: a review

Biodiversity of amoebae and amoeba-resisting bacteria in a hospital water network.

Free-living amoebae and their intracellular pathogenic microorganisms: risks for water quality.

Biodiversity of amoebae and amoebae-resisting bacteria in a drinking water treatment plant.

Amoebae in domestic water systems: resistance to disinfection treatments and implication in Legionella persistence