Microbiomics Overview

This page catalogs all publicly available Microbiomics datasets in the Hibernomics Database. Currently, 36 species have microbiomics data, comprising 23 datasets from peer-reviewed publications. Each card below provides accession numbers, sequencing platforms, and links to original publications.

36
Species with Data
Out of 59 hibernating species
23
Total Datasets
Curated from literature
20
SRA Available
With public archive accessions
16
Literature Only
DOI-linked publications

Species with Microbiomics Data

MIC
Available

A. davidianus | Andrias davidianus

Amphibia > Caudata > Cryptobranchidae

16S rRNA (MiSeq, growth stages)

AccessionPRJNA1332065
Platform16S rRNA (MiSeq, growth stages)
Publication10.3389/fmicb.2023.1052824
Platform 2Shotgun Metagenomics (antibiotics, gut)
2023-03-01 Browse SRA
MIC
Literature

A. sinensis | Andrias sinensis

Reptilia > Crocodilia > Alligatoridae

16S + Shotgun Metagenomics

Platform16S + Shotgun Metagenomics
Publication10.3389/fmicb.2019.02409
2019-10-15 View Paper
MIC
Available

B. gargarizans | Bufo gargarizans

Amphibia > Anura > Bufonidae

16S rRNA (metamorphosis, 4 stages)

AccessionPRJNA666156
Platform16S rRNA (metamorphosis, 4 stages)
Publication10.1007/s00203-018-1523-1
Dataset 2PRJNA1143048
Platform 2Metagenomics (3 habitats, MAGs)
2018-09-01 Browse SRA
MIC
Available

B. pewzowi | Bufo pewzowi

Amphibia > Anura > Bufonidae

16S rRNA (GSA, 57 samples, Tarim Desert)

AccessionCRA016285
Platform16S rRNA (GSA, 57 samples, Tarim Desert)
Publication10.1111/1749-4877.12963
2025-02-01 Browse SRA
MIC
Literature

B. raddei | Bufo raddei

Amphibia > Anura > Bufonidae

16S rRNA (heavy metal pollution, GI microbiota)

Platform16S rRNA (heavy metal pollution, GI microbiota)
Publication10.1016/j.toxlet.2016.07.003
Platform 216S rRNA (nitrate exposure, tadpoles)
2016-07-16 View Paper
MIC
Literature

C. hemileucurus | Calypte hemileucurus

Aves > Apodiformes > Trochilidae

See paper for details

PlatformSee paper for details
Publication10.1098/rspb.2018.2295
N/A View Paper
MIC
Available

C. medius | Cheirogaleus medius

Mammalia > Primates > Cheirogaleidae

Illumina (16S V4, seasonal)

AccessionPRJNA1189778
PlatformIllumina (16S V4, seasonal)
Publication10.1007/s10764-024-00477-9
2024-12-01 Browse SRA
MIC
Available

C. septempunctata | Coccinella septempunctata

Insecta > Coleoptera > Coccinellidae

Illumina (16S rRNA)

AccessionPRJNA963975
PlatformIllumina (16S rRNA)
Publication10.1038/s41598-023-49885-6
2024-01-02 Browse SRA
MIC
Available

D. nitedula | Dryomys nitedula

Mammalia > Rodentia > Gliridae

Illumina (metagenomic pathogen screening)

AccessionPRJNA1241767
PlatformIllumina (metagenomic pathogen screening)
Publication10.1007/s10344-025-02008-0
2025-01-01 Browse SRA
MIC
Literature

E. carinata | Eremias carinata

Reptilia > Squamata > Colubridae

16S rRNA (HiSeq)

Platform16S rRNA (HiSeq)
Publication10.7717/peerj.6658
2019-03-29 View Paper
MIC
Available

E. europaeus | Erinaceus europaeus

Mammalia > Eulipotyphla > Erinaceidae

Illumina (16S V3-V4, wild mammals)

AccessionPRJNA1191222
PlatformIllumina (16S V3-V4, wild mammals)
Publication10.1016/j.watres.2025.124990
2024-01-01 Browse SRA
MIC
Available

E. multiocellata | Eremias multiocellata

Reptilia > Squamata > Lacertidae

16S rRNA + Metagenomics

AccessionCRA011520
Platform16S rRNA + Metagenomics
Publication10.1186/s40168-023-01736-2
2024-02-01 Browse SRA
MIC
Available

E. quercinus | Eliomys quercinus

Mammalia > Rodentia > Gliridae

Illumina (metagenomic pathogen screening)

AccessionPRJNA1241767
PlatformIllumina (metagenomic pathogen screening)
Publication10.1007/s10344-025-02008-0
2025-01-01 Browse SRA
MIC
Literature

F. multistriata | Fejervarya multistriata

Amphibia > Anura > Dicroglossidae

Metagenomics (gut microbiome, bile acids, tadpoles)

PlatformMetagenomics (gut microbiome, bile acids, tadpoles)
Publication10.1016/j.cbpa.2025.02.003
2025-06-01 View Paper
MIC
Available

I. tridecemlineatus | Ictidomys tridecemlineatus

Mammalia > Rodentia > Sciuridae

16S rRNA (MiSeq, gut microbiome)

AccessionPRJNA676170
Platform16S rRNA (MiSeq, gut microbiome)
Publication10.1186/s42523-021-00117-0
2021-08-01 Browse SRA
MIC
Available

L. agilis | Lacerta agilis

Reptilia > Squamata > Lacertidae

PacBio + Illumina (WGS)

AccessionPRJNA837731
PlatformPacBio + Illumina (WGS)
Publication10.5187/jast.2022.e55
Platform 2UPLC-MS/MS + RNA-seq
2022-09-30 Browse SRA
MIC
Literature

L. sylvaticus | L. sylvaticus

Amphibia > Anura > Hylidae

16S rRNA (skin microbiome, reviewed)

Platform16S rRNA (skin microbiome, reviewed)
Publication10.1016/j.dci.2023.104733
2023-10-01 View Paper
MIC
Literature

M. auratus | Mesocricetus auratus

Mammalia > Rodentia > Cricetidae

16S rRNA (5 GI regions)

Platform16S rRNA (5 GI regions)
Publication10.1002/2211-5463.13869
2024-08-04 View Paper
MIC
Literature

M. himalayana | Marmota himalayana

Mammalia > Rodentia > Sciuridae

Shotgun Metagenomics (45 fecal samples)

PlatformShotgun Metagenomics (45 fecal samples)
Publication10.1016/j.bsheal.2025.09.003
2025-09-08 View Paper
MIC
Literature

M. murinus | Microcebus murinus

Mammalia > Primates > Cheirogaleidae

16S rRNA + metagenomic sequencing (gut microbiome)

Platform16S rRNA + metagenomic sequencing (gut microbiome)
Publication10.3724/ahr.2095-0357.2024.0027
2024-01-01 View Paper
MIC
Literature

N. natrix | Natrix natrix

Reptilia > Squamata > Colubridae

Culture + MALDI-TOF

PlatformCulture + MALDI-TOF
Publication10.1007/s00284-020-02021-3
2020-04-22 View Paper
MIC
Available

N. noctula | Nyctalus noctula

Mammalia > Chiroptera > Vespertilionidae

Illumina (16S rRNA, V3-V4)

AccessionPRJNA1173750
PlatformIllumina (16S rRNA, V3-V4)
Publication10.3390/vetsci12060559
2025-06-01 Browse SRA
MIC
Literature

N. parkeri | Nanorana parkeri

Amphibia > Anura > Ranidae

16S rRNA + metagenomic sequencing (gut microbiome)

Platform16S rRNA + metagenomic sequencing (gut microbiome)
Publication10.3724/ahr.2095-0357.2024.0027
2024-01-01 View Paper
MIC
Literature

P. mucosus | Ptyas mucosus

Reptilia > Squamata > Colubridae

16S rRNA + Metabolomics

Platform16S rRNA + Metabolomics
Publication10.1007/s00253-023-12524-1
2023-04-18 View Paper
MIC
Literature

P. nigromaculatus | Pelophylax nigromaculatus

Amphibia > Anura > Ranidae

16S rRNA (atrazine exposure & recovery)

Platform16S rRNA (atrazine exposure & recovery)
Publication10.1016/j.scitotenv.2022.154307
Platform 216S rRNA (intestinal histology, SCFAs)
2022-01-01 View Paper
MIC
Available

P. nuttallii | Peromyscus nuttallii

Aves > Caprimulgiformes > Caprimulgidae

16S rRNA (gut microbiome, agricultural habitat)

AccessionPRJNA1068550
Platform16S rRNA (gut microbiome, agricultural habitat)
2024-01-01 Browse SRA
MIC
Available

R. dybowskii | Rana dybowskii

Amphibia > Anura > Ranidae

16S rRNA (MiSeq, 7 developmental stages)

AccessionPRJNA428920
Platform16S rRNA (MiSeq, 7 developmental stages)
Publication10.1016/j.scitotenv.2020.140142
Dataset 2PRJNA516808
Platform 216S rRNA (captivity & season)
2020-06-13 Browse SRA
MIC
Available

R. ferrumequinum | Rhinolophus ferrumequinum

Mammalia > Chiroptera > Rhinolophidae

16S rRNA (MiSeq, seasonal)

AccessionSRR8756041
Platform16S rRNA (MiSeq, seasonal)
Publication10.3389/fmicb.2019.02247
Platform 216S rRNA (captivity)
2019-10-01 Browse SRA
MIC
Literature

T. aculeatus | Tachyglossus aculeatus

Mammalia > Monotremata > Tachyglossidae

16S rRNA (gestation stability)

Platform16S rRNA (gestation stability)
Publication10.1002/mbo3.1392
Platform 216S rRNA (lactation, pouch)
2023-12-14 View Paper
MIC
Available

T. carolina | Terrapene carolina

Reptilia > Testudines > Emydidae

Illumina (16S rRNA)

AccessionPRJNA924021
PlatformIllumina (16S rRNA)
Publication10.3389/fvets.2024.1276436
2024-06-06 Browse SRA
MIC
Available

T. sibiricus | Tamias sibiricus

Mammalia > Rodentia > Sciuridae

16S rRNA (MiSeq, seasonal)

AccessionPRJNA264760
Platform16S rRNA (MiSeq, seasonal)
Publication10.1007/s00248-021-01877-7
2021-08-01 Browse SRA
MIC
Available

U. americanus | Ursus americanus

Mammalia > Carnivora > Ursidae

Illumina (16S rRNA)

AccessionPRJEB29403
PlatformIllumina (16S rRNA)
Publication10.1371/journal.pone.0345317
2025-04-20 Browse SRA
MIC
Literature

U. arctos | Ursus arctos

Mammalia > Carnivora > Ursidae

MiSeq (16S rRNA, V3-V4)

PlatformMiSeq (16S rRNA, V3-V4)
Publication10.1016/j.celrep.2016.01.026
2016-02-23 View Paper
MIC
Available

U. maritimus | Ursus maritimus

Mammalia > Carnivora > Ursidae

16S rRNA (MiSeq)

AccessionPRJNA542176
Platform16S rRNA (MiSeq)
Publication10.1038/s41598-021-02657-6
2021-01-11 Browse SRA
MIC
Literature

U. parryii | Urocitellus parryii

Mammalia > Rodentia > Sciuridae

Culture-based (cecal microbiota)

PlatformCulture-based (cecal microbiota)
Publication10.1128/AEM.01537-14
2014-09-01 View Paper
MIC
Available

U. thibetanus | Ursus thibetanus

Mammalia > Carnivora > Ursidae

Illumina MiSeq (16S V3-V4)

AccessionPRJNA407583
PlatformIllumina MiSeq (16S V3-V4)
Publication10.1007/s00438-016-1282-0
Dataset 2PRJNA1154995
Platform 2Shotgun Metagenomics
2017-04-01 Browse SRA

Explore Other Omics Types

Genomics
58 species
Transcriptomics
40 species
Epigenomics
11 species
Proteomics
19 species
Metabolomics
19 species
Microbiomics
36 species