Extensive research in well-studied animal models underscores the importance of commensal gastrointestinal (gut) microbes to animal physiology. Gut microbes have been shown to impact dietary digestion, mediate infection, and even modify behavior and cognition. Given the large physiological and pathophysiological contribution microbes provide their host, it is reasonable to assume that the vertebrate gut microbiome may also impact the fitness, health and ecology of wildlife. In accordance with this expectation, an increasing number of investigations have considered the role of the gut microbiome in wildlife ecology, health, and conservation. To help promote the development of this nascent field, we need to dissolve the technical barriers prohibitive to performing wildlife microbiome research. The present review discusses the 16S rRNA gene microbiome research landscape, clarifying best practices in microbiome data generation and analysis, with particular emphasis on unique situations that arise during wildlife investigations. Special consideration is given to topics relevant for microbiome wildlife research from sample collection to molecular techniques for data generation, to data analysis strategies. Our hope is that this article not only calls for greater integration of microbiome analyses into wildlife ecology and health studies but provides researchers with the technical framework needed to successfully conduct such investigations.
Aquatic bacteria frequently are divided into lifestyle categories oligotroph or copiotroph. Oligotrophs have proportionately fewer transcriptional regulatory genes than copiotrophs and are generally non-motile/chemotactic. We hypothesized that the absence of chemotaxis/motility in oligotrophs prevents them from occupying nutrient patches long enough to benefit from transcriptional regulation. We first confirmed that marine oligotrophs are generally reduced in genes for transcriptional regulation and motility/chemotaxis. Next, using a non-motile oligotroph (Ca. Pelagibacter st. HTCC7211), a motile copiotroph (Alteromonas macleodii st. HOT1A3), and [ 14 C]L-alanine, we confirmed that L-alanine catabolism is not transcriptionally regulated in HTCC7211 but is in HOT1A3. We then found that HOT1A3 took 2.5-4 min to initiate L-alanine oxidation at patch L-alanine concentrations, compared to <30 s for HTCC7211. By modelling cell trajectories, we predicted that, in most scenarios, non-motile cells spend <2 min in patches, compared to >4 min for chemotactic/motile cells. Thus, the time necessary for transcriptional regulation to initiate prevents transcriptional regulation from being beneficial for non-motile oligotrophs. This is supported by a mechanistic model we developed, which predicted that HTCC7211 cells with transcriptional regulation of L-alanine metabolism would produce 12% of their standing ATP stock upon encountering an L-alanine patch, compared to 880% in HTCC7211 cells without transcriptional regulation.
Aquatic bacteria are frequently divided into the lifestyle categories oligotroph or copiotroph, reflecting adaptations to low and high nutrient availability. In aquatic ecosystems, copiotrophy is associated with chemotaxis and motility, which cells use to find and occupy high-nutrient patches. Oligotrophs have proportionately fewer transcriptional regulatory proteins than copiotrophs, and some have been shown to constitutively express genes involved in the uptake and oxidation of carbon compounds. We hypothesized that the absence of chemotaxis/motility in oligotrophs might prevent them from occupying nutrient patches long enough to benefit from transcriptional regulation. To test this hypothesis, we measured uptake and oxidation of a radiolabeled amino acid, [14C]L-alanine, by a non-motile oligotroph (Ca. Pelagibacter st. HTCC7211) and a motile copiotroph (Alteromonas macleodii st. HOT1A3). We found that L-alanine catabolism is not transcriptionally regulated in HTCC7211 but is in HOT1A3, initiating within 2.5 - 4 min, as supported by RT-qPCR experiments. L-alanine uptake in HTCC7211 was modulated within 30s by low-amplitude (2-fold) post-translational regulation, a conclusion supported by quantitative analysis with a mechanistic model. By modeling cell trajectories under a range of patch conditions, we predicted that, in most scenarios, non-motile cells spend <2 min in patches, while chemotactic/motile cells occupy patches >4 mins. We conclude that the time necessary to initiate transcriptional regulation prevents non-motile oligotrophs, which drift with currents, from benefiting from transcriptional regulation, but instead have low-amplitude post-translational regulation that can take advantage of their transient passage through a patch.
Here, we report a draft genome sequence of Plesiomonas shigelloides strain zfcc0051, an isolate derived from zebrafish ( Danio rerio ) feces. The genome consists of 115 contigs (>500 bp) and has a total assembly length of 4,041,537 bases.
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