Four-stranded mini microtubules formed by Prosthecobacter BtubAB show dynamic instability.

Microtubules, the dynamic, yet stiff hollow tubes built from αß-tubulin protein heterodimers, are thought to be present only in eukaryotic cells. Here, we report a 3.6-Å helical reconstruction electron cryomicroscopy structure of four-stranded mini microtubules formed by bacterial tubulin-like Prosthecobacter dejongeii BtubAB proteins. Despite their much smaller diameter, mini microtubules share many key structural features with eukaryotic microtubules, such as an M-loop, alternating subunits, and a seam that breaks overall helical symmetry. Using in vitro total internal reflection fluorescence microscopy, we show that bacterial mini microtubules treadmill and display dynamic instability, another hallmark of eukaryotic microtubules. The third protein in the btub gene cluster, BtubC, previously known as "bacterial kinesin light chain," binds along protofilaments every 8 nm, inhibits BtubAB mini microtubule catastrophe, and increases rescue. Our work reveals that some bacteria contain regulated and dynamic cytomotive microtubule systems that were once thought to be only useful in much larger and sophisticated eukaryotic cells.

Planctomycetes and eukaryotes: a case of analogy not homology.

Planctomycetes, Verrucomicrobia and Chlamydia are prokaryotic phyla, sometimes grouped together as the PVC superphylum of eubacteria. Some PVC species possess interesting attributes, in particular, internal membranes that superficially resemble eukaryotic endomembranes. Some biologists now claim that PVC bacteria are nucleus-bearing prokaryotes and are considered evolutionary intermediates in the transition from prokaryote to eukaryote. PVC prokaryotes do not possess a nucleus and are not intermediates in the prokaryote-to-eukaryote transition. Here we summarise the evidence that shows why all of the PVC traits that are currently cited as evidence for aspiring eukaryoticity are either analogous (the result of convergent evolution), not homologous, to eukaryotic traits; or else they are the result of horizontal gene transfers.

Microbial fucoidan degradation by Luteolibacter algae H18 with deacetylation.

A bacterial strain that assimilates fucoidan from Cladosiphon okamuranus as sole carbon source was isolated as Luteolibacter algae H-18. It was found that it degraded fucoidan by intracellular enzymes, and that the degradation reactions were catalyzed by multiple enzymes. One enzyme, designated fraction B, was established to exhibit the deacetylation reaction of fucoidan. Other enzyme(s), designated fraction A, catalyzed the reaction(s) lowering the molecular weight of fucoidan.

High-throughput single-cell cultivation reveals the underexplored rare biosphere in deep-sea sediments along the Southwest Indian Ridge.

Microorganisms in the deep sea play vital roles in marine ecosystems. However, despite great advances brought by high throughput sequencing and metagenomics, only a small portion of microorganisms living in the environment can be cultivated in the laboratory and systematically studied. In this study, an improved high-throughput microfluidic streak plate (MSP) platform was developed to speed up the isolation of microorganisms from deep-sea sediments and evaluated with deep-sea sediments collected from the Southwest Indian Ridge (SWIR). Based on our previously reported MSP method, we improved its isolation efficiency with a semi-automated droplet picker and improved humidity control to enable long-term cultivation with a low-nutrient medium for up to five months according to the slow-growing nature of most deep-sea species. The improved MSP method allows the isolation of microbes by selection and investigation of microbial diversity by high throughput sequencing of the pooled sample cultures. By picking individual droplets and scale-up cultivation, a total of 772 strains that were taxonomically assigned to 70 species were isolated from the deep-sea sediments in the SWIR, including 15 potential novel species. On the other hand, based on 16S rRNA gene amplicon sequencing analysis, the microbial diversity of the SWIR was studied and documented with culture-dependent and independent methods in this study. The superiority of the MSP platform in revealing the rare biosphere was also evaluated based on amplicon sequencing. The results show that droplet-based single-cell cultivation of the MSP has a much higher ability than traditional agar plate cultivation in obtaining microbial species and more than 90% of operational taxonomic units (OTUs) detected in the MSP pool belong to the rare biosphere. Our results indicate the high robustness and efficiency of the improved MSP platform in revealing the environmentally rare biosphere, especially for slow-growing species. Overall, the MSP platform has a superior ability to recover microbial diversity than conventional agar plates and it was found to hold great potential for recovering rare microbial resources from various environments.

Preparation and preservation of viable Akkermansia muciniphila cells for therapeutic interventions.

The anaerobic gut bacterium Akkermansia muciniphila is a well-characterised member of the mucosal microbiota and has shown to be a gut symbiont in human. A. muciniphila has been negatively associated with obesity and its associated metabolic disorders in various human cohorts while treatment with A. muciniphila cells reversed highfat diet-induced obesity and its associated metabolic disorders in mouse models. Therefore, administration of A. muciniphila has been suggested as a possible new therapeutic treatment for these omnipresent diseases. Here we describe a potentially scalable workflow for the preparation and preservation of high numbers of viable cells of A. muciniphila obtained from 1 l laboratory scale growth under strict anaerobic conditions for therapeutic interventions. This resulted in viable A. muciniphila cells with high yields and very high stability, with up to 97.9±4.5% survival for a time period of 1 year at -80 °C in glycerol-amended medium. Moreover, various quality assessment and control procedures were developed to ensure the use of viable cells of A. muciniphila. Several microscopic, culturing, and molecular approaches were applied to monitor the presence, abundance and recovery of A. muciniphila before, during, and after its administration to high-fat treated mice. We show that viable A. muciniphila cells can be recovered from caecal and colon content (up to 1×1010 cells/g), testifying for the efficiency of the described workflow.

Are uncultivated bacteria really uncultivable?

Many strategies have been used to increase the number of bacterial cells that can be grown from environmental samples but cultivation efficiency remains a challenge for microbial ecologists. The difficulty of cultivating a fraction of bacteria in environmental samples can be classified into two non-exclusive categories. Bacterial taxa with no cultivated representatives for which appropriate laboratory conditions necessary for growth are yet to be identified. The other class is cells in a non-dividing state (also known as dormant or viable but not culturable cells) that require the removal or addition of certain factors to re-initiate growth. A number of strategies, from simple to high throughput techniques, are reviewed that have been used to increase the cultivation efficiency of environmental samples. Some of the underlying mechanisms that contribute to the success of these cultivation strategies are described. Overall this review emphasizes the need of researchers to first understand the factors that are hindering cultivation to identify the best strategies to improve cultivation efficiency.