DOI: 10.5061/dryad.x3ffbg7sk
title: Absence of a functional gut microbiome impairs host amino acid metabolism in the Pacific spiny dogfish (Squalus suckleyi)

description: Nitrogen recycling and amino acid synthesis are two notable ways in which
 the gut microbiome can contribute to host metabolism, and these processes
 are especially important in nitrogen-limited animals. Marine elasmobranchs
 are nitrogen-limited as they require substantial amounts of this element
 to support urea-based osmoregulation. However, following
 antibiotic-induced depletion of the gut microbiome elasmobranchs are known
 to experience a significant decline in circulating urea and seem to employ
 compensatory nitrogen conservation strategies such as reduced urea and
 ammonia excretion. We hypothesized that the elasmobranch gut microbiome
 transforms dietary and recycled nutrients into amino acids, supporting
 host carbon and nitrogen balance. Here, we found that depleting the gut
 microbiome of Pacific spiny dogfish (Squalus suckleyi) resulted in a
 significant reduction in the incorporation of supplemented dietary 15N
 into plasma amino acids, notably those linked to nitrogen handling and
 energy metabolism, but had no effect on gut amino acid transport. These
 results demonstrate the importance of gut microbes to host amino acid
 pools and the unique nitrogen-handling strategy of marine elasmobranchs.
 More broadly, these results elucidate how the gut microbiome contributes
 to organismal homeostasis, which is likely a ubiquitous phenomenon across
 animal populations.
description: # Absence of a functional gut microbiome impairs host amino acid
 metabolism in the Pacific spiny dogfish (Squalus suckleyi) The data
 package contains three datasets: 1. N_compounds.csv 2.
 delta15Naminoacids.csv 3. fluxdata.csv Datasets of the recorded variables
 **(1) N_compounds.csv** This dataset contains δ15N values for bulk tissue
 as well as protein, free amino acids, urea, and ammonia from various
 dogfish tissues following either a saline or antibiotic treatment.
 Variable names with descriptions: Dogfish_ID: unique ID code for each fish
 from which tissues were collected. Treatment: Either 72_Control or
 72_Antibiotic, indicating whether the individual was apart of the control
 or antibiotic treated groups. Tissue: the tissue that was collected and
 analyzed for δ15N values. ant_intest = anterior intestinal fold;
 mid_intest = middle intestinal fold; post_intest = posterior intestinal
 fold; liver = liver; plasma = plasma; muscle = white muscle. N_component:
 the nitrogenous compound that was isolated from the sample and analyzed
 for δ15N values. amino = free amino acids; protein = protein; whole = bulk
 tissue; ammonia = ammonia; urea = urea. delta_N15: the δ15N values that
 correspond to each individual nitrogenous compound within a tissue
 sampled. **(2) delta15Naminoacids.csv** This dataset contains δ15N values
 for individual amino acids from various dogfish tissues following either a
 saline or antibiotic treatment. Variable names with descriptions: fish_ID:
 unique ID code for each fish from which tissues were collected. treatment:
 Either C (control) or ABX (antibiotic), indicating whether the individual
 was apart of the control or antibiotic treated groups. tissue: the tissue
 that was collected and analyzed for δ15N values. liver = liver; plasma =
 plasma; muscle = white muscle. sample: whether the sample was taken as a
 baseline (BL) at the time of feeding (only for the plasma) or 72 hours
 after feeding during the dissection (TD). aminoacid: the amino acid that
 was measured, indicated by the standard three letter code for that amino
 acid. delta: the δ15N values that correspond to each individual amino acid
 within the tissue sampled. **(3) fluxdata.csv** This dataset contains flux
 data for the amino acids leucine and alanine across the intestine of
 Pacific spiny dogfish following either a saline or antibiotic treatment.
 Variable names with descriptions: ID: unique ID code for each fish from
 which tissues were collected. Treatment: Either Control or ABX
 (antibiotic), indicating whether the individual was apart of the control
 or antibiotic treated groups. Concentration: the concentration of the
 amino acid added to the mucosal side of the flux chamber in, mM, either 1
 or 10. amino: the amino acid that was measured, indicated by the standard
 three letter code for that amino acid. app: serosal appearance rate (nmol
 h-1 cm-2) tissue: tissue accumulation (pmol h-1 g tissue-1)