Extensive horizontal gene transfer in cheese-associated bacteria.

Acquisition of genes through horizontal gene transfer (HGT) allows microbes to rapidly gain new capabilities and adapt to new or changing environments. Identifying widespread HGT regions within multispecies microbiomes can pinpoint the molecular mechanisms that play key roles in microbiome assembly. We sought to identify horizontally transferred genes within a model microbiome, the cheese rind. Comparing 31 newly sequenced and 134 previously sequenced bacterial isolates from cheese rinds, we identified over 200 putative horizontally transferred genomic regions containing 4733 protein coding genes. The largest of these regions are enriched for genes involved in siderophore acquisition, and are widely distributed in cheese rinds in both Europe and the US. These results suggest that HGT is prevalent in cheese rind microbiomes, and that identification of genes that are frequently transferred in a particular environment may provide insight into the selective forces shaping microbial communities

The Irreversible Loss of a Decomposition Pathway Marks the Single Origin of an Ectomycorrhizal Symbiosis

Microbial symbioses have evolved repeatedly across the tree of life, but the genetic changes underlying transitions to symbiosis are largely unknown, especially for eukaryotic microbial symbionts. We used the genus Amanita, an iconic group of mushroom-forming fungi engaged in ectomycorrhizal symbioses with plants, to identify both the origins and potential genetic changes maintaining the stability of this mutualism. A multi-gene phylogeny reveals one origin of the symbiosis within Amanita, with a single transition from saprotrophic decomposition of dead organic matter to biotrophic dependence on host plants for carbon. Associated with this transition are the losses of two cellulase genes, each of which plays a critical role in extracellular decomposition of organic matter. However a third gene, which acts at later stages in cellulose decomposition, is retained by many, but not all, ectomycorrhizal species. Experiments confirm that symbiotic Amanita species have lost the ability to grow on complex organic matter and have therefore lost the capacity to live in forest soils without carbon supplied by a host plant. Irreversible losses of decomposition pathways are likely to play key roles in the evolutionary stability of these ubiquitous mutualisms.Organismic and Evolutionary Biolog

Biotic Interactions Shape the Ecological Distributions of Staphylococcus Species.

Many metagenomic sequencing studies have observed the presence of closely related bacterial species or genotypes in the same microbiome. Previous attempts to explain these patterns of microdiversity have focused on the abiotic environment, but few have considered how biotic interactions could drive patterns of microbiome diversity. We dissected the patterns, processes, and mechanisms shaping the ecological distributions of three closely related Staphylococcus species in cheese rind biofilms. Paradoxically, the most abundant species (S. equorum) is the slowest colonizer and weakest competitor based on growth and competition assays in the laboratory. Through in vitro community reconstructions, we determined that biotic interactions with neighboring fungi help resolve this paradox. Species-specific stimulation of the poor competitor by fungi of the genus Scopulariopsis allows S. equorum to dominate communities in vitro as it does in situ Results of comparative genomic and transcriptomic experiments indicate that iron utilization pathways, including a homolog of the S. aureus staphyloferrin B siderophore operon pathway, are potential molecular mechanisms underlying Staphylococcus-Scopulariopsis interactions. Our integrated approach demonstrates that fungi can structure the ecological distributions of closely related bacterial species, and the data highlight the importance of bacterium-fungus interactions in attempts to design and manipulate microbiomes.ImportanceDecades of culture-based studies and more recent metagenomic studies have demonstrated that bacterial species in agriculture, medicine, industry, and nature are unevenly distributed across time and space. The ecological processes and molecular mechanisms that shape these distributions are not well understood because it is challenging to connect in situ patterns of diversity with mechanistic in vitro studies in the laboratory. Using tractable cheese rind biofilms and a focus on coagulase-negative staphylococcus (CNS) species, we demonstrate that fungi can mediate the ecological distributions of closely related bacterial species. One of the Staphylococcus species studied, S. saprophyticus, is a common cause of urinary tract infections. By identifying processes that control the abundance of undesirable CNS species, cheese producers will have more precise control on the safety and quality of their products. More generally, Staphylococcus species frequently co-occur with fungi in mammalian microbiomes, and similar bacterium-fungus interactions may structure bacterial diversity in these systems

Transposable Element Dynamics among Asymbiotic and Ectomycorrhizal Amanita Fungi

Transposable elements (TEs) are ubiquitous inhabitants of eukaryotic genomes and their proliferation and dispersal shape genome architectures and diversity. Nevertheless, TE dynamics are often explored for one species at a time and are rarely considered in ecological contexts. Recent work with plant pathogens suggests a link between symbiosis and TE abundance. The genomes of pathogenic fungi appear to house an increased abundance of TEs, and TEs are frequently associated with the genes involved in symbiosis. To investigate whether this pattern is general, and relevant to mutualistic plant-fungal symbioses, we sequenced the genomes of related asymbiotic (AS) and ectomycorrhizal (ECM) Amanita fungi. Using methods developed to interrogate both assembled and unassembled sequences, we characterized and quantified TEs across three AS and three ECM species, including the AS outgroup Volvariella volvacea. The ECM genomes are characterized by abundant numbers of TEs, an especially prominent feature of unassembled sequencing libraries. Increased TE activity in ECM species is also supported by phylogenetic analysis of the three most abundant TE superfamilies; phylogenies revealed many radiations within contemporary ECM species. However, the AS species Amanita thiersii also houses extensive amplifications of elements, highlighting the influence of additional evolutionary parameters on TE abundance. Our analyses provide further evidence for a link between symbiotic associations among plants and fungi, and increased TE activity, while highlighting the importance individual species’ natural histories may have in shaping genome architecture

Deciphering the Microbiome: Integrating Theory, New Technologies, and Inclusive Science

The diversity and functional significance of microbiomes have become increasingly clear through the extensive sampling of Earth\u27s many habitats and the rapid adoption of new sequencing technologies. However, much remains unknown about what makes a “healthy” microbiome, how to restore a disrupted microbiome, and how microbiomes assemble. In December 2019, we convened a workshop that focused on how to identify potential “rules of life” that govern microbiome structure and function. This collection of mSystems Perspective pieces reflects many of the main challenges and opportunities in the field identified by both in-person and virtual workshop participants. By borrowing conceptual and theoretical approaches from other fields, including economics and philosophy, these pieces suggest new ways to dissect microbiome patterns and processes. The application of conceptual advances, including trait-based theory and community coalescence, is providing new insights on how to predict and manage microbiome diversity and function. Technological and analytical advances, including deep transfer learning, metabolic models, and advances in analytical chemistry, are helping us sift through complex systems to pinpoint mechanisms of microbiome assembly and dynamics. Integration of all of these advancements (theory, concepts, technology) across biological and spatial scales is providing dramatically improved temporal and spatial resolution of microbiome dynamics. This integrative microbiome research is happening in a new moment in science where academic institutions, scientific societies, and funding agencies must act collaboratively to support and train a diverse and inclusive community of microbiome scientists

The effects of intramuscular tenotomy on the lengthening characteristics of tibialis posterior: high versus low intramuscular tenotomy

BACKGROUND: Lengthening of soft-tissue contractures is frequently required in children with a wide variety of congenital and acquired deformities. However, little is known about the biomechanics of surgical procedures which are commonly used in contracture surgery, or if variations in technique may have a bearing on surgical outcomes. We investigated the hypothesis that the site of intramuscular tenotomy (IMT) within the muscle-tendon-unit (MTU) of the tibialis posterior (TP) would affect the lengthening characteristics. METHODS: We performed a randomized trial on paired cadaver tibialis posterior muscle-tendon-units (TP-MTUs). By random allocation, one of each pair of formalin-preserved TP-MTUs received a high IMT, and the other a low IMT. These were individually tensile-tested with an Instron(®) machine under controlled conditions. A graph of load (Newtons) versus displacement (millimetres) was generated for each pair of tests. The differences in lengthening and load at failure for each pair of TP-MTUs were noted and compared using paired t tests. RESULTS: We found 48% greater lengthening for low IMT compared to high IMT for a given load (P = 0.004, two tailed t test). Load at failure was also significantly lower for the low IMT. These findings confirm our hypothesis that the site of the tenotomy affects the amount of lengthening achieved. This may contribute to the reported variability in clinical outcome. CONCLUSIONS: Understanding the relationship between tenotomy site and lengthening may allow surgeons to vary the site of the tenotomy in order to achieve pre-determined surgical goals. It may be possible to control the surgical "dose" by altering the position of the intramuscular tenotomy within the muscle-tendon-unit

Individual and non‐additive effects of exotic sap‐feeders on root functional and mycorrhizal traits of a shared conifer host

Forest pests drive tree mortality through disruption of functional traits linked to nutrient acquisition, growth and reproduction. The impacts of attack by individual or multiple above‐ground herbivores on root functional traits critical to tree health have received little attention. This is especially true for exotic herbivores, organisms often found in disturbed forests. We excavated whole‐root systems from eastern hemlock (Tsuga canadensis) individuals experimentally infested with hemlock woolly adelgid (HWA: Adelges tsugae) and elongate hemlock scale (EHS: Fiorina externa) individually, or in combination, for periods of 2 and 4 years. Below‐ground root biomass, functional traits and storage nutrients were measured to assess impacts of herbivory. We also quantified ectomycorrhizal fungal (EMF) colonisation of fine roots and used culture‐independent methods to examine EMF diversity. Trees infested with HWA had a greater root mass fraction (root to total biomass ratio), although feeding had no observable effects on root functional traits (e.g. specific root length) or on resource allocation to roots. HWA feeding did significantly reduce EMF colonisation of hemlock fine roots, though surprisingly, EMF diversity and that of other fungal associates were unaffected. In contrast to HWA, EHS (alone or in conjunction with HWA) feeding had no observable effect on below‐ground traits or EMF colonisation alone; however, its presence mediated HWA effects when trees were co‐infested. Simultaneous infestation within the same year yielded significant reductions in EMF colonisation, whereas prior EHS attack weakened HWA effects. Our results collectively suggest that prior EHS attack dampens the impact of HWA on below‐ground functional traits. This highlights how the timing and sequence of herbivore arrival can alter plant‐mediated interactions between herbivores and their effects on above–below‐ground linkages and associated tree health

The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods

An expert panel was convened in September 2019 by The International Scientific Association for Probiotics and Prebiotics (ISAPP) to develop a definition for fermented foods and to describe their role in the human diet. Although these foods have been consumed for thousands of years, they are receiving increased attention among biologists, nutritionists, technologists, clinicians and consumers. Despite this interest, inconsistencies related to the use of the term ‘fermented’ led the panel to define fermented foods and beverages as “foods made through desired microbial growth and enzymatic conversions of food components”. This definition, encompassing the many varieties of fermented foods, is intended to clarify what is (and is not) a fermented food. The distinction between fermented foods and probiotics is further clarified. The panel also addressed the current state of knowledge on the safety, risks and health benefits, including an assessment of the nutritional attributes and a mechanistic rationale for how fermented foods could improve gastrointestinal and general health. The latest advancements in our understanding of the microbial ecology and systems biology of these foods were discussed. Finally, the panel reviewed how fermented foods are regulated and discussed efforts to include them as a separate category in national dietary guidelines

The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods

An expert panel was convened in September 2019 by The International Scientific Association for Probiotics and Prebiotics (ISAPP) to develop a definition for fermented foods and to describe their role in the human diet. Although these foods have been consumed for thousands of years, they are receiving increased attention among biologists, nutritionists, technologists, clinicians and consumers. Despite this interest, inconsistencies related to the use of the term ‘fermented’ led the panel to define fermented foods and beverages as “foods made through desired microbial growth and enzymatic conversions of food components”. This definition, encompassing the many varieties of fermented foods, is intended to clarify what is (and is not) a fermented food. The distinction between fermented foods and probiotics is further clarified. The panel also addressed the current state of knowledge on the safety, risks and health benefits, including an assessment of the nutritional attributes and a mechanistic rationale for how fermented foods could improve gastrointestinal and general health. The latest advancements in our understanding of the microbial ecology and systems biology of these foods were discussed. Finally, the panel reviewed how fermented foods are regulated and discussed efforts to include them as a separate category in national dietary guidelines

Control of bacterial nitrate assimilation by stabilization of G-quadruplex DNA

Here we present a chemical-biology study in the model soil bacterium Paracoccus denitrificans, where we show ligand-specific control of nitrate assimilation. Stabilization of a G-quadruplex in the promoter region of the nas genes, encoding the assimilatory nitrate/nitrite reductase system, is achieved using known quadruplex ligands and results in attenuation of gene transcription