Biology subjects

Bohannan, B. J.

Publications and source records attributed to Bohannan, B. J..

4 recordsLinked to original sources

bioRxiv2025

Spontaneous mutant in threespine stickleback connects endosome trafficking disorders and inflammatory bowel diseases via changes in the gut microbiome

Endosomes are organelles that sort and traffic materials to different cellular compartments to enable performance of other organelles. One group of organelles supported by endosomes are lysosome related organelles (LROs) - which perform specialized functions using endocytosed or recycled materials from endosomes. LROs include melanosomes, lytic granules, platelet dense granules, lamellar bodies, and more. Individuals with endosome trafficking disorders commonly present with oculocutaneous albinism due to insufficient trafficking to - and maturation of - melanosomes. While the loss of pigment is an easily identifiable phenotype, mutations in endosome trafficking can also cause multi-organ system symptoms due to more broad disruption of LROs. Different endosome trafficking mutations impact LRO maturation at different degrees of severity and can impact a subset or all LROs leading to a wide range of symptomologies. Endosome trafficking disorders can present with oculocutaneous albinism (caused by mutated melanosomes), blood diathesis (caused by mutated platelet dense granules), pulmonary fibrosis (caused by mutated lamellar bodies), or chronic inflammation and inflammatory bowel disease (IBD) (caused by mutated lytic granules), as well as other symptoms. The shared inflammatory patterns of Hermansky-Pudlak Syndrome (HPS) and Inflammatory Bowel Disease (IBD) are well studied. However, impacts of this shared gastrointestinal inflammation on the gut microbiome remain unexplored. Using a spontaneously identified mutant family of threespine stickleback fish, we characterize changes in LROs and symptoms of oculocutaneous albinism. We further demonstrate that the shared gastrointestinal phenotypes of HPS and IBD extend to the gut microbiome showing similar shifts in microbial communities consistent with IBD. We argue endosome trafficking models should be explored as models to study the gut microbiome in addition to inflammatory phenotypes in IBD, and importantly, be used to test microbial/dietary interventions for both IBD and endosome trafficking disorders.

genetics↗

bioRxiv2025

Aquaculture facility-specific microbiota shape the zebrafish gut microbiome

BackgroundEnvironmental microbiomes, such as those in recirculating aquaculture systems (RAS), can play a key role in shaping host-associated microbial communities. In zebrafish (Danio rerio) research, these interactions can introduce uncontrolled sources of variation, potentially confounding experimental outcomes across multiple facilities. Despite widespread zebrafish use in microbiome studies, few have characterized the microbial composition of both tank water and fish across multiple independent facilities to evaluate the consequences of environmental microbiome variation on the host microbiome. ResultsWe compared water and zebrafish gut microbiomes across five aquaculture facilities--two in the United States and three in Norway--using a nested sampling design and 16S rRNA gene sequencing. Alpha diversity was consistently higher in tank water than in fish guts, and beta diversity metrics revealed distinct clustering by sample type, facility, and location. Differences in microbial community composition were significant across facilities, with both water and fish samples exhibiting facility-specific profiles. Similarity Percentage analysis identified taxonomic groups driving these differences, while Fast Expectation-Maximization for Microbial Source Tracking detected measurable contributions of tank water microbiota to zebrafish gut communities. Bray-Curtis dissimilarity values were lowest between fish and water from the same tank and increased with geographic and facility distance, indicating local microbial overlap. Relative abundance patterns and ordination plots further supported distinct and structured microbial assemblages across systems. ConclusionsThis study demonstrates that zebrafish aquaculture systems harbor unique microbial communities shaped by both environmental and geographic factors, with tank water acting as a potential source of gut-associated microbes. These findings underscore the importance of incorporating environmental microbiome assessments into zebrafish experimental design, particularly for studies focused on host-microbe interactions. Without such consideration, unaccounted variation in environmental microbiota may affect microbiome composition and reduce cross-study reproducibility. Moving forward, standardized reporting of environmental conditions and microbial composition across facilities will be critical for strengthening reproducibility and interpretation in zebrafish microbiome research.

microbiology↗

bioRxiv2021

Maintaining grass coverage increases methane uptake in Amazonian pasture soils

Cattle ranching is the largest driver of deforestation in the Brazilian Amazon. The rainforest- to-pasture conversion affects the methane cycle in upland soils, changing it from sink to source of atmospheric methane. However, it remains unknown if management practices could reduce the impact of land-use on methane cycling. In this work, we evaluated how pasture management can regulate the soil methane cycle either by maintaining continuous grass coverage on pasture soils, or by liming the soil to amend acidity. Methane fluxes from forest and pasture soils were evaluated in moisture-controlled greenhouse experiments with and without grass cover (Urochloa brizantha cv. Marandu) or liming. In parallel, we assessed changes in the soil microbial community structure of both bare pasture soil as well as rhizosphere soil through high throughput sequencing of the 16S rRNA gene, and quantified the methane cycling microbiota by their respective marker genes related to methane generation (mcrA) or oxidation (pmoA). The experiments used soils from eastern and western Amazonia, and concurrent field studies allowed us to confirm greenhouse data. The presence of a grass cover not only increased methane uptake by up to 35% in pasture soils, but also reduced the abundance of the methane-producing community. In the grass rhizosphere this reduction was up to 10-fold. Methane-producing archaea belonged to the genera Methanosarcina sp., Methanocella sp., Methanobacterium sp., and Rice Cluster I. Further, we showed that liming compromised the capacity of forest and pasture soils to be a sink for methane, and instead converted formerly methane-consuming forest soils to become methane sources in only 40-80 days. Our results demonstrate that pasture management that maintains grass coverage can mitigate soil methane emissions, if compared to a bare pasture soil.

microbiology↗

bioRxiv2019

Linking microbial communities to ecosystem functions: what we can learn from genotype-phenotype mapping in organisms

Microorganisms mediate many important ecosystem functions, yet it remains unclear to what extent microbial diversity or community composition is important for determining the rates of ecosystem-scale functions. This uncertainty limits our ability to predict and manage crucial microbially-mediated processes, such as nutrient loss and greenhouse gas emissions. Our lack of understanding stems from the relatively large diversity of microorganisms, the difficulty in directly identifying functional groups, and our limited ability to manipulate microbial community attributes. For this reason, we propose that integrating traditional biodiversity-ecosystem function research with ideas from genotype-phenotype mapping could provide the new perspective our discipline needs. We identify three insights from genotype-phenotype mapping that could be useful for microbial biodiversity-ecosystem function studies: the concept of \"agnostic\" mapping, the use of more powerful ways to account for multiple comparisons, and the incorporation of covariates into models of ecosystem function. We illustrate the potential for these approaches to elucidate microbial biodiversity-ecosystem function relationships by analyzing a subset of published data measuring methane oxidation rates from incubations of tropical soil. We assert that combining the approaches of traditional biodiversity-ecosystem function research with ideas from genotype-phenotype mapping will not only generate novel hypotheses about how complex microbial communities drive ecosystem function, but also help scientists predict and manage changes to ecosystem functions resulting from human activities.

ecology↗