Motility genes are associated with the occurrence of -associated gut microbes.

Recent work highlighted the role of motility genes in dispersing fly-associated microbes and their spread between hosts. We investigated whether bacterial genes encoding motility are associated with the occurrence of bacteria above passive dispersal levels in the gut of wild . We revisited 16S amplicon and shotgun metagenome data of wild flies and correlated four genera of bacteria (, , , and ) with motility genes.

Dietary B vitamins influence the preference for dietary yeast.

The microbiota influences the dietary preference for yeast (DPY). We previously identified four transposon insertion mutants in that significantly influence fly DPY, and three of these insertions were in genes that are associated with thiamine metabolism. Here, we tested if thiamine influences fly DPY in monoassociated flies.

Humidity determines penetrance of a latitudinal gradient in genetic selection on the microbiota by .

Unlabelled: The fruit fly is a model for understanding how hosts and their microbial partners interact as the host adapts to wild environments. These interactions are readily interrogated because of the low taxonomic and numeric complexity of the flies' bacterial communities. Previous work has established that host genotype, the environment, diet, and interspecies microbial interactions can all influence host fitness and microbiota composition, but the specific processes and characters mediating these processes are incompletely understood.

Flagellar Genes Are Associated with the Colonization Persistence Phenotype of the Drosophila melanogaster Microbiota.

In this work, we use Drosophila melanogaster as a model to identify bacterial genes necessary for bacteria to colonize their hosts independent of the bulk flow of diet. Early work on this model system established that dietary replenishment drives the composition of the D. melanogaster gut microbiota, and subsequent research has shown that some bacterial strains can stably colonize, or persist within, the fly independent of dietary replenishment.

Bacterial Metabolism and Transport Genes Are Associated with the Preference of Drosophila melanogaster for Dietary Yeast.

Many animal traits are influenced by their associated microorganisms ("microbiota"). To expand our understanding of the relationship between microbial genotype and host phenotype, we report an analysis of the influence of the microbiota on the dietary preference of the fruit fly Drosophila melanogaster. First, we confirmed through experiments on flies reared bacteria-free ("axenic") or in monoassociation with two different strains of bacteria that the microbiota significantly influences fruit fly dietary preference across a range of ratios of dietary yeast:dietary glucose.

The impact of Rhodiola rosea on biomarkers of diabetes, inflammation, and microbiota in a leptin receptor-knockout mouse model.

Type 2 diabetes is the most prevalent endocrine disease in the world, and recently the gut microbiota have become a potential target for its management. Recent studies have illustrated that this disease may predispose individuals to certain microbiome compositions, and treatments like metformin have been shown to change gut microbiota and their associated metabolic pathways. However, given the limitations and side effects associated with pharmaceuticals currently being used for therapy of diabetes, there is a significant need for alternative treatments.

Increased Microbial Diversity and Decreased Prevalence of Common Pathogens in the Gut Microbiomes of Wild Turkeys Compared to Domestic Turkeys.

Turkeys (Meleagris gallopavo) provide a globally important source of protein and constitute the second most important source of poultry meat in the world. Bacterial diseases are common in commercial poultry production, causing significant production losses for farmers. Due to the increasingly recognized problems associated with large-scale/indiscriminate antibiotic use in agricultural settings, poultry producers need alternative methods to control common bacterial pathogens.

An altered microbiome in a Parkinson's disease model Drosophila melanogaster has a negative effect on development.

Parkinson's disease (PD) is the second most common neurodegenerative disease, besides Alzheimer's Disease, characterized by multiple symptoms, including the well-known motor dysfunctions. It is well-established that there are differences in the fecal microbiota composition between Parkinson's disease (PD) patients and control populations, but the mechanisms underlying these differences are not yet fully understood. To begin to close the gap between description and mechanism we studied the relationship between the microbiota and PD in a model organism, Drosophila melanogaster.

Microbiota Influences Fitness and Timing of Reproduction in the Fruit Fly Drosophila melanogaster.

Associated microorganisms ("microbiota") play a central role in determining many animals' survival and reproduction characteristics. The impact of these microbial influences on an animal's fitness, or population growth, in a given environment has not been defined as clearly. We focused on microbiota-dependent host fitness by measuring life span and fecundity in Drosophila melanogaster fruit flies reared individually with 14 different bacterial species.

Spatiotemporal variation in the fecal microbiota of mule deer is associated with proximate and future measures of host health.

Background: Mule deer rely on fat and protein stored prior to the winter season as an energy source during the winter months when other food sources are sparse. Since associated microorganisms ('microbiota') play a significant role in nutrient metabolism of their hosts, we predicted that variation in the microbiota might be associated with nutrient storage and overwintering in mule deer populations. To test this hypothesis we performed a 16S rRNA marker gene survey of fecal samples from two deer populations in the western United States before and after onset of winter.

Genome Sequence of Lactiplantibacillus plantarum DmPark25_157, a Bacterial Strain Isolated from Drosophila melanogaster.

We present the genome sequence of a bacterial strain isolated from mutants of as part of efforts to better understand the microbial communities in We isolated and sequenced a strain. We present a preliminary comparative analysis with a closely related strain.

A culture-independent approach to understanding the role of soil fungal communities in Bromus tectorum stand failure.

Cheatgrass (Bromus tectorum L.) is an invasive annual grass (Poaceae) that has colonized large portions of the Intermountain West. Cheatgrass stand failures have been observed throughout the invaded region, the cause of which may be related to the presence of several species of pathogenic fungi in the soil or surface litter.

Genome Sequence of Acetobacter tropicalis DmPark25_167, a Bacterium Isolated from a Drosophila melanogaster Genetic Model of Parkinson's Disease.

Here, we report the genome of DmPark25_167, a bacterial strain isolated from a mutant. The mutant is an established genetic model of Parkinson's disease. DmPark25_167 has duplicated methionine metabolism and type IV secretion gene alleles compared with another strain of .

Gut microbiota differs a decade after bariatric surgery relative to a nonsurgical comparison group.

Background: Few studies have assessed differences in the gut microbiota composition after bariatric surgery in the long term or whether differences are correlated with remission of type 2 diabetes.

Objectives: This observational study assessed differences in the gut microbiota between individuals at up to 13 years after surgery and a comparison group of individuals with severe obesity. The relationship between type 2 diabetes remission and the gut microbiota was also assessed.

Genetic Influences of the Microbiota on the Life Span of Drosophila melanogaster.

To better understand how associated microorganisms ("microbiota") influence organismal aging, we focused on the model organism We conducted a metagenome-wide association (MGWA) as a screen to identify bacterial genes associated with variation in the life span. The results of the MGWA predicted that bacterial cysteine and methionine metabolism genes influence fruit fly longevity. A mutant analysis, in which flies were inoculated with strains bearing mutations in various methionine cycle genes, confirmed a role for some methionine cycle genes in extending or shortening fruit fly life span.

The microbiota influences the Drosophila melanogaster life history strategy.

Organisms are locally adapted when members of a population have a fitness advantage in one location relative to conspecifics in other geographies. For example, across latitudinal gradients, some organisms may trade off between traits that maximize fitness components in one, but not both, of somatic maintenance or reproductive output. Latitudinal gradients in life history strategies are traditionally attributed to environmental selection on an animal's genotype, without any consideration of the possible impact of associated microorganisms ("microbiota") on life history traits.

Microbiome composition shapes rapid genomic adaptation of .

Population genomic data has revealed patterns of genetic variation associated with adaptation in many taxa. Yet understanding the adaptive process that drives such patterns is challenging; it requires disentangling the ecological agents of selection, determining the relevant timescales over which evolution occurs, and elucidating the genetic architecture of adaptation. Doing so for the adaptation of hosts to their microbiome is of particular interest with growing recognition of the importance and complexity of host-microbe interactions.

Bacterial Communities in the Alpaca Gastrointestinal Tract Vary With Diet and Body Site.

Gut -associated microbes ('gut microbiota') impact the nutrition of their hosts, especially in ruminants and pseudoruminants that consume high-cellulose diets. Examples include the pseudoruminant alpaca. To better understand how body site and diet influence the alpaca microbiota, we performed three 16S rRNA gene surveys.

Genomic Structural Variations Within Five Continental Populations of .

Chromosomal structural variations (SV) including insertions, deletions, inversions, and translocations occur within the genome and can have a significant effect on organismal phenotype. Some of these effects are caused by structural variations containing genes. Large structural variations represent a significant amount of the genetic diversity within a population.

Bacterial Methionine Metabolism Genes Influence Drosophila melanogaster Starvation Resistance.

Animal-associated microorganisms (microbiota) dramatically influence the nutritional and physiological traits of their hosts. To expand our understanding of such influences, we predicted bacterial genes that influence a quantitative animal trait by a comparative genomic approach, and we extended these predictions via mutant analysis. We focused on starvation resistance (SR).

A Metagenome-Wide Association Study and Arrayed Mutant Library Confirm Lipopolysaccharide Genes Are Necessary for Association with .

A metagenome wide association (MGWA) study of bacterial host association determinants in predicted that LPS biosynthesis genes are significantly associated with host colonization. We were unable to create site-directed mutants for each of the predicted genes in , so we created an arrayed transposon insertion library using DsW_054 isolated from Creation of the DsW_054 gene knock-out library was performed by combinatorial mapping and Illumina sequencing of random transposon insertion mutants. Transposon insertion locations for 6,418 mutants were successfully mapped, including hits within 63% of annotated genes in the DsW_054 genome.

MAGNAMWAR: an R package for genome-wide association studies of bacterial orthologs.

Summary: Here we report on an R package for genome-wide association studies of orthologous genes in bacteria. Before using the software, orthologs from bacterial genomes or metagenomes are defined using local or online implementations of OrthoMCL. These presence-absence patterns are statistically associated with variation in user-collected phenotypes using the Mono-Associated GNotobiotic Animals Metagenome-Wide Association R package (MAGNAMWAR).

Draft Genome Sequence of DmW181, a Bacterium Isolated from Wild .

The draft genome sequence of DmW181, an anaerobic bacterium isolate from wild flies, is reported here. Strain DmW181 possesses genes for sialic acid and mannose metabolism. The assembled genome is 3,201,429 bp, with 3,454 predicted genes.