The effect of the use of commercial tempeh starter on the diversity of Rhizopus tempeh in Indonesia

At present, only a single Rhizopus species, R. microsporus, can be found in fresh tempeh produced in Java, Indonesia. The loss of diversity of Rhizopus in tempeh has been associated with the widespread use of commercial tempeh starter in Indonesia since the 2000s. However, the identities of the previous Rhizopus strains associated with tempeh, which have been preserved in a culture collection in Indonesia, have not been verified. The present study aimed to verify the identities of 22 Rhizopus strains isolated from tempeh produced using the traditional tempeh starters from the 1960s to the 2000s. Phylogenetic analysis based on the ITS regions in the rRNA gene sequence data, revealed that the Rhizopus strains belonged to the species R. arrhizus (five strains); R. delemar (14 strains); and R. microsporus (three strains). Verification of the identities of these Rhizopus strains in the present study confirmed the loss of diversity of Rhizopus species in tempeh produced in Indonesia, particularly in Java. Our findings confirmed that the morphological changes in Rhizopus species isolated from tempeh as a result of centuries of domestication.

Range extension of Ichthyophis multicolor Wilkinson et al., 2014 to India and first molecular identification of Ichthyophis moustakius Kamei et al., 2009

We report a substantial range extension of Ichthyophis multicolor Wilkinson, Presswell, Sherratt, Papadopoulou & Gower, 2014, with new material from Mizoram State, Northeast India. The species was previously known only from its type locality more than 800 km away in Ayeyarwady Region, Myanmar. The species was identified by both its morphology and 16s rRNA gene sequence data. One of the studied individuals represents the largest known specimen for the species (total length = 501 mm; mid-body width = 18.8 mm). Brief comparisons of I. multicolor with the sympatric as well as parapatric congeners in the region, and first barcode data for I. moustakius Kamei, Wilkinson, Gower & Biju, 2009 are also presented.

Identification and Removal of Potential Contaminants in 16S rRNA Gene Sequence Data Sets from Low-Microbial-Biomass Samples: an Example from Mosquito Tissues

The study of tissue-associated microbiota from mosquitoes (primarily from the gut) has grown significantly in the last several years. Mosquito tissue samples represent a challenge for researchers given their low microbial biomass and similar taxonomic composition commonly found in the laboratory environment and in molecular reagents.

Phylogenetic Integration Reveals the Zebrafish Core Microbiome and Its Sensitivity to Environmental Exposures

Zebrafish are increasingly used to study how environmental exposures impact vertebrate gut microbes. However, we understand little about which microbial taxa are common to the zebrafish gut across studies and facilities. Here, we define the zebrafish core gut microbiome to resolve microbiota that are both relatively robust to study or facility effects and likely to drive proper microbiome assembly and functioning due to their conservation. To do so, we integrated publicly available gut microbiome 16S gene sequence data from eight studies into a phylogeny and identified monophyletic clades of gut bacteria that are unexpectedly prevalent across individuals. Doing so revealed 585 core clades of bacteria in the zebrafish gut, including clades within Aeromonas, Pseudomonas, Cetobacterium, Shewanella, Chitinibacter, Fluviicola, Flectobacillus, and Paucibacter. We then applied linear regression to discern which of these core clades are sensitive to an array of different environmental exposures. We found that 200 core clades were insensitive to any exposure we assessed, while 134 core clades were sensitive to more than two exposures. Overall, our analysis defines the zebrafish core gut microbiome and its sensitivity to exposure, which helps future studies to assess the robustness of their results and prioritize taxa for empirical assessments of how gut microbiota mediate the effects of exposure on the zebrafish host.

A Multi-Scale Approach to Modeling E. coli Chemotaxis

The degree to which we can understand the multi-scale organization of cellular life is tied to how well our models can represent this organization and the processes that drive its evolution. This paper uses Vivarium—an engine for composing heterogeneous computational biology models into integrated, multi-scale simulations. Vivarium’s approach is demonstrated by combining several sub-models of biophysical processes into a model of chemotactic E. coli that exchange molecules with their environment, express the genes required for chemotaxis, swim, grow, and divide. This model is developed incrementally, highlighting cross-compartment mechanisms that link E. coli to its environment, with models for: (1) metabolism and transport, with transport moving nutrients across the membrane boundary and metabolism converting them to useful metabolites, (2) transcription, translation, complexation, and degradation, with stochastic mechanisms that read real gene sequence data and consume base pairs and ATP to make proteins and complexes, and (3) the activity of flagella and chemoreceptors, which together support navigation in the environment.

Minutes of the International Committee on Systematics of Prokaryotes online discussion on the proposed use of gene sequences as type for naming of prokaryotes, and outcome of vote

The International Committee on Systematics of Prokaryotes has held an electronic discussion on proposals to amend the International Code of Nomenclature of Prokaryotes in order to allow the use of gene sequence data as type. The scientific discussion is reported. Subsequently members of the International Committee on Systematics of Prokaryotes voted on these proposals, which were rejected.