Microbe Profiles

Candida glabrata is a fungal microbe associated with multiple vertebrate microbiomes and their terrestrial environments. In humans, the species has emerged as an opportunistic pathogen that now ranks as the second-leading cause of candidiasis in Europe and North America (Beardsley et al. Med Mycol 2024, 62). People at highest risk of infection include the elderly, immunocompromised individuals and/or long-term residents of hospital and assisted-living facilities. C. glabrata is intrinsically drug-resistant, metabolically versatile and able to avoid detection by the immune system. Analyses of its 12.3 Mb genome indicate a stable pangenome Marcet-Houben et al. (BMC Biol 2022, 20) and phylogenetic affinity with Saccharomyces cerevisiae. Recent phylogenetic analyses suggest reclassifying C. glabrata as Nakaseomyces glabratus Lakashima and Sugita (Med Mycol J 2022, 63: 119-132).

Bacteriophage ϕ6 is a segmented dsRNA virus with a lipid envelope, which are unusual traits in bacterial viruses but common in eukaryotic viruses. This uniqueness allowed ϕ6 and its Pseudomonad hosts to serve as a molecular model for RNA genetics, mutation, replication, packaging, and reassortment in both bacterial and eukaryotic viruses. However, an additional uniqueness of ϕ6, created by its high mutation rate, was its use as an experimental system to study key questions such as the evolution of sex (segment reassortment), host–pathogen interactions, mutational load, rates of adaptation, genetic and phenotypic complexity, and game theory.

The bacterial family   Lactobacillaceae   (the lactobacilli) occupy a unique role in microbiology due to their beneficial role in both human cultural history and biology, from the food preservation of hunter gatherers-turned-farmers, through the prevention of scurvy in seafarers exploring new worlds, and the health-promoting properties of species that colonize the human body as well as animals that are important for agriculture and pollination. The almost bewildering phenotypic and genomic complexity of the former genus   Lactobacillus   was recently reconciled with molecular taxonomy and phylogeny to establish robust genera comprising the   Lactobacillaceae  , whose main features are summarized in this Microbe Profile.

  Ruminococcus gnavus   is a human gut symbiont, part of the infant and adult gut microbiota and associated with intestinal and extra-intestinal disorders.   R. gnavus   mechanisms of adaptation to the gut are strain-specific and underpinned by the capacity of   R. gnavus   strains to utilize mucin and dietary glycans and produce bacteriocins and adhesins. Several potential mediators underpinning the association between   R. gnavus   strains and diseases have been identified, including the capacity to elicit a pro- or anti-inflammatory host response and modulate host metabolism, secondary bile acids and tryptophan metabolic pathways. Based on increasing evidence from metagenomics studies in humans and functional investigations in vitro and in mouse models,   R. gnavus   is emerging as a main player in influencing health and disease outcomes from infants to the elderly.

  Streptococcus pneumoniae   may inhabit the upper respiratory tract of humans without causing harm but it also causes diseases with high morbidity and mortality. It has excellent adaptive capabilities thanks to its ability to shuffle its genetic content by acquiring and incorporating DNA from other bacteria and is highly competent for genetic transformation. Sugar sensing, cleavage and transport ensure its fitness and survival in the host, and intracellular survival in macrophages has been linked to virulence. The polysaccharide capsule and toxin pneumolysin are the most important virulence determinants. Polysaccharide-based vaccines provide protection against the serotypes represented in vaccine formulations.

Euglena gracilis is a unicellular photosynthetic eukaryotic flagellate of the Discoba supergroup, which also encompasses Kinetoplastida and Diplonema. Plastids have green algal origin and are secondarily acquired. The nuclear genome is extremely large and many genes suggest multiple endosymbiotic/gene transfer events, i.e. derivation from prokaryotes of various lineages. E. gracilis is remarkably robust and can proliferate in environments contaminated with heavy metals and acids. Extraordinary metabolic plasticity and a mixotrophic lifestyle confers an ability to thrive in a broad range of environments, as well as facilitating production of many novel metabolites, making Euglena of considerable biotechnological importance.

Pectobacterium atrosepticum is part of a larger family of soft rot bacteria ( Pectobacteriaceae ) that cause disease on a wide range of crops worldwide. They are closely related to members of the Enterobacteriaceae and, as the plant pathogens and plant associated members of the group, form part of a continuum towards opportunistic and more devastating animal and human pathogens. Many of the horizontally acquired islands present in the genome of P. atrosepticum are directly responsible for life on plants. These include genes for a plethora of plant cell wall degrading enzymes, plant toxins, siderophores etc., which are exported by multiple secretion systems under a highly coordinated regulation system.

Gigaspora margarita is a cosmopolitan arbuscular mycorrhizal fungus, which - as an obligate symbiont- requires being associated to a host plant to accomplish its life cycle. It is characterized by huge white spores, the development of extraradical auxiliary cells, and the lack of intraradical vesicles. Its genome is dominated by transposable elements and is one of the largest fungal genomes so far sequenced. G. margarita has the peculiar feature to host taxonomically different endobacteria in its cytoplasm. The development of a cured line has allowed us to demonstrate how the endobacteria have a positive impact on the fungal physiology and -with a cascade effect- on the mycorrhizal plant.

  Legionella pneumophila   is an environmental bacterium that parasitizes aquatic protozoa and uses the same processes to infect humans. The facultative intracellular pathogen causes a life-threatening pneumonia with possible systemic complications. The co-evolution with protozoa is reflected in an armoury of bacterial effectors, and many of these type IV-secreted proteins have likely been acquired by interdomain horizontal gene transfer (HGT) from hosts. The unique features of   L. pneumophila   are the largest bacterial effector repertoire known to date, subversion of virtually all eukaryotic signalling pathways and acquisition of eukaryotic enzyme activities used to manipulate the host cell to the pathogen’s advantage.

  Buchnera aphidicola   is an obligate endosymbiont of aphids that cannot be cultured outside of hosts. It exists as diverse strains in different aphid species, and phylogenetic reconstructions show that it has been maternally transmitted in aphids for >100 million years.   B. aphidicola   genomes are highly reduced and show conserved gene order and no gene acquisition, but encoded proteins undergo rapid evolution. Aphids depend on   B. aphidicola   for biosynthesis of essential amino acids and as an integral part of embryonic development. How   B. aphidicola   populations are regulated within hosts remains little known.