DOI: 10.5061/dryad.7m0cfxq2m
title: Microbiome diversity and zoonotic bacterial pathogen prevalence in Peromyscus mice from agricultural landscapes and synanthropic habitat

description: Rodents are key reservoirs of zoonotic pathogens and play an important
 role in disease transmission to humans. Importantly, anthropogenic
 land-use change has been found to increase the abundance of rodents that
 thrive in human-built environments (synanthropic rodents), particularly
 rodent reservoirs of zoonotic disease. Anthropogenic environments also
 affect the microbiome of synanthropic wildlife, influencing wildlife
 health and potentially introducing novel pathogens. Our objective was to
 examine the effect of agricultural development and synanthropic habitat on
 microbiome diversity and the prevalence of zoonotic bacterial pathogens in
 wild Peromyscus mice to better understand the role of these rodents in
 pathogen maintenance and transmission. We conducted 16S amplicon
 sequencing on fecal samples using long-read Nanopore sequencing technology
 to characterize the rodent microbiome. We compared microbiome diversity
 and composition between forest and synanthropic habitats in agricultural
 and undeveloped landscapes and screened for putative pathogenic bacteria.
 Microbiome richness, diversity, and evenness were higher in the
 agricultural landscape and synanthropic habitat compared to
 undeveloped-forest habitat. Microbiome composition also differed
 significantly between agricultural and undeveloped landscapes and forest
 and synanthropic habitat. We detected overall low diversity and abundance
 of putative pathogenic bacteria, though putative pathogens were more
 likely to be found in mice from the agricultural landscape. Our findings
 show that landscape- and habitat-level anthropogenic factors affect
 Peromyscus microbiomes and suggest that landscape-level agricultural
 development may be important to predict zoonotic pathogen prevalence.
 Ultimately, understanding how anthropogenic land-use change and
 synanthropy affect rodent microbiomes and pathogen prevalence is important
 to managing transmission of rodent-borne zoonotic diseases to humans.
description: Peromyscus mice were live-trapped and fecal samples were
 collected for microbiome analysis. Data was collected during field data
 collection documenting the date and location of trapped animals, body
 measurements (body mass, body length), sex, reproductive status, and
 samples collected. Data was also recorded during the lab processing of the
 collected fecal samples for DNA extraction, library preparation, and
 Nanopore sequencing of barcoded libraries.
description: # Minnesota Peromyscus mouse microbiome
 These data were collected
 in June-August 2019 during live trapping of small mammals in central and
 northern Minnesota. Trapping was conducted at two locations: Cedar Creek
 Ecosystem Science Reserve in central MN and Itasca Biological Station and
 Laboratories and Itasca State Park in northern MN. Animals were trapped in
 forest habitat and around human habitation and buildings at both
 locations. Only mice of the genus Peromyscus were sampled (Peromyscus
 leucopus and Peromyscus maniculatus). Blood, feces, and a tissue sample
 were collected from each animal, sex and reproductive condition were
 assessed, and the mass and body length were recorded. Trapping was
 conducted at the same sites in June, July, and August at Cedar Creek.
 Trapping was only conducted in July at Itasca. Mice captured at Cedar
 Creek were identified with a uniquely numbered ear tag to identify
 individuals at subsequent recaptures. ## Description of the data and file
 structure File: MN_Pero_field_data_v10.8.19.csv *Note: Data values that
 were not recorded or do not apply to a given entry are filled with
 "NA" | **Variable** | **Description** | **Units** | |
 :------------------ |
 :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | :----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | ID | Unique row identifier | numeric | | date\_data\_entry | Date data was digitized from paper data sheet. | MM/DD/YYYY format | | data\_enterer | Initials of individual who digitized the paper data sheet. | | | processing\_date | Date of animal capture. | MM/DD/YYYY format | | location | Field site location. | Options are IBSL (Itasca Biological Station and Laboratories) or CCESR (Cedar Creek Ecosystem Science Reserve) | | field\_site\_detail | Detailed name of field site. | | | field\_site | Field site group - multiple detailed names make up one group. Each group had 50 traps set. | | | weather | Arbitrary identifier of current weather at time of animal processing | | | processing\_time | Start time (AM hours) the specific animal was processed | | | handler | Initials of individual who handled and sampled the animal | | | data\_recorder | Initials of individual who recorded the data on a paper datasheet in the field | | | trap\_number | Unique identifer of the trap the animal was caught in. Traps were placed in a grid where each column had a unique letter and the traps were numbered sequentially. Some trap numbers are noted with an asterisk (\*). I don't know why anymore. | | | animals\_per\_trap | Number of animals in the trap, Sherman traps were used so more than 1 animal per trap was rare | | | capture | Status of the animal, whether it was new (N) to the study, a recapture (R) from a previous month's trapping, or a week recapture (WR) indicating an animal that was captured at that site in the previous day of sampling (all sites were sampled for 2 days) | | | species | Species of the captured animal | Options: Pspp (Peromyscus species), Myodes\_spp, Zapus (Zapus hudsonius), Microtus\_spp, Tstr (Tamias striatus), Thud (Tamiasciurus hudsonicus), Bbrev (Blarina brevicauda), Scin (Sorex cinerus), Amphibian | | ear\_tag\_number | Unique identifer for voles captured at CCESR. Sites were sampled in June, July, and August at CCESR. Ear tags were not used at IBSL because trapping was only conducted in one month. | | | body\_mass | Mass of animal | grams (g) | | sex | Animal sex | 1=Male, 0=Female | | testes | If male, were scrotal testes observed | 1=Yes, 0=No | | perforate | If female, was the vagina perforate (open, indicating a receptive reproductive female) | 1=Yes, 0=No | | nipples | If female, were nipples visible above the fur | 1=Yes, 0=No | | lactating | If female, was she lactacting (evidenced by hair loss and crusting around the nipples) | 1=Yes, 0=No | | pregnant | If female, was she visibly pregnant | 1=Yes, 0=No | | pelage | Coat color of animal, used to assess age. Juveniles are Grey, subadults are P (post-juvenile molt), adults are Brown, older adults may be Orange | Options: G, P, B, O | | body\_length | Body length from nose to base of tail, measured with calipers while the animal was unconcious | millimeters (mm) | | dna\_number | Sample ID number for DNA sample (ear punch) | | | blood\_number | Sample ID number for blood sample (retro-orbital eye bleed, saved on Whatman filter paper) | | | eye\_bed | Which eye (left or right, from the animal's perspective) was the blood sample taken from | Options: L, R | | feces\_number | Sample ID number for fecal sample | | | fleas | Were fleas observed on the animal | 1=Yes, 0=No | | botflies | Number of botflies found on the animal | count | | botscars | Number of botfly scars (wounds indicating a botfly had previously emerged) on the animal | count | | wounds | Number of wounds on the animal | count | | ticks\_head | Count of ticks (larval, nymph, or adult) found on the animal's head/ears | count | | ticks\_neck | Count of ticks (larval, nymph, or adult) found on the animal's neck | count | | tick\_taken\_number | Sample ID for engorged tick collected from the animal | | | dead | Was the animal dead (either when discovered in the trap or died during processing) | 1=Yes, 0=No | | dead\_in\_trap | Was the animal dead when the trap was checked in the morning | 1=Yes, 0=No | | rigor\_mortis | Was the animal in rigor mortis when it was found dead | 1=Yes, 0=No | | vd\_eye\_number | Sample ID of eye lens collected from deceased animals or 'NOT COLLECTED' if entire carcass was collected but eye lens was not extracted | | | Notes | Additional notes recorded by handler | | File: Fecal_sample_processing.csv File includes: Fecal sample field data, DNA extraction data, and Oxford Nanopore Technologies sequencing data These data document the laboratory processing of fecal samples used for bacterial gut microbiome sequencing of wild Peromyscus mice captured in Minnesota in 2019. Data in columns (location, field_site, species, ear_tag_number, fecal_sample_id, fecal_sample_number) were derived from the MN_Pero_field_data file and were copied to this file (with no edits) for easy reference. Data in the columns (sample_mass, dna_extraction_date, dna_extraction_method_processer, original_dna_concentration, dna_sample_id, sequence_run_id, sequence_date_barcode, notes) are unique to this file and document the laboratory processing (dna extraction) and sequencing (Oxford Nanopore Technologies R9 flowcell) of fecal samples. *Note: Data values that were not recorded or do not apply to a given entry are filled with "NA" | **Data** | **Description** | **Units** | | :--------------------------------- | :---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | :--------------------------- | | location | Location of field site. | Options: CCESR, IBSL | | field\_site | Name of field site | | | species | Animal species. Peromyscus mice were not identified to species and are therefore recorded only as "pspp" for Peromyscus species | | | ear\_tag\_number | Unique animal ear tag identifer. Animals at IBSL were not recaptured and were not given ear tags. All individuals sampled at IBSL are unique. | | | fecal\_sample\_id | Sample ID for fecal sample | | | fecal\_sample\_number | Sample ID as just a number for fecal sample. Supplementary samples were collected from animals recaptured on the second trapping day to increase sample material (designated as ###-2). Supplementary samples were combined with the original sample prior to DNA extraction. | | | sample\_mass | Mass of fecal sample | grams (g) | | dna\_extraction\_date | Date of DNA extraction | Date recorded as MM.DD.YY | | dna\_extraction\_method\_processer | Method of DNA extraction (options: manual or with Qiacube robotic workstation) and initials of person(s) running the extraction | | | original\_dna\_concentration | DNA concentration after extraction as quantified by an Invitrogen Qubit Fluorometer | nanograms/microlitre (ng/uL) | | dna\_sample\_id | Sample ID for extracted DNA sample | | | sequence\_run\_id | Unique identifier for the 16S bacterial DNA sequencing run using an Oxford Nanopore Technologies R9 flowcell including the sample site/location where the samples were collected and the sequencing run date | | | sequence\_date\_barcode | Date of sequencing run \_ Sample Barcode (to identify individual samples sequenced on a single flowcell) | Date recorded as MMDDYY | | notes | Additional notes added by processor | | ## Code/Software Code available on GitHub: Raw sequence data is accessioned with the NCBI Sequence Read Archive: