Animal models have been critical tools since the early days of scientific discovery. Today they are indispensable in biomedical research contributing to our understanding of the functions of genes, the etiology and mechanisms of different diseases, and the effectiveness and the toxicities of medicines and chemicals. The genomes of the major model organisms have been sequenced, verifying a high level of genetic conservation among model organisms and humans.

Labome surveys literature for instruments and reagents. Labome has surveyed formal publications citing animal models to provide an overview of animal models in publications (Table 1). The survey results indicate that mouse is the overwhelmingly preferred laboratory animal; the most widely used mouse and rat strains are C57BL/6 mice, BALB/c mice, Sprague-Dawley rats and Wistar rats. Other strains, such as A/J mice, CD1 mice, and ICR mice, were also used. The majority of these animals are supplied by four major providers, The Jackson Laboratory, Charles River Laboratories, Taconic Biosciences and Harlan Laboratories. The aforementioned animal models are used for research in immunology, oncology, physiology, pathology, and increasingly, neuroscience. Some of the interesting mouse models are discussed later in this article.

Albinism of laboratory rodents: The majority of laboratory rodents are albinos, due to a common mutation in tyrosinase gene in all albino laboratory rat strains [18] and in at least some of the albino mouse strains [19]. Tyrosinase is the rate-limiting enzyme in the production of melanin pigment. The prevalence of albinism among laboratory rodents is because many of the earliest established strains were albino, and also albinism is an easy selection marker in the early days.

Mice are the most frequently cited animal model in biomedical publications (Table 1). Most of the publications surveyed by Labome cited various strains of mice (along with rats, and occasionally rabbits, ferrets, guinea pigs, and rhesus macaque). Tables 2 and 3 list the number of articles annotated with specific medical subject headings (MeSH) or search parameters related to mice in the PUBMED database. It is clear that research conducted on mouse models continues to be an important part of our collective research efforts and knowledge, even with ongoing efforts to replacing animal testing with cell culture models or computational prediction, especially for toxicological studies [20].

The prevalence of mouse models in biomedical research is not surprising given that mice require relatively inexpensive care, reproduce quickly, and have a high genetic similarity to humans. Technologies, such as transgenic methods, have been very well developed in mouse models to study the genetics and the functions of specific genes. Mouse models of many human diseases have also been developed to advance the studies of disease pathogenesis, and to evaluate the effectiveness and toxicities of various candidate drugs. However, laboratory mice are generally raised in abnormally hygienic facilities that differ from the pathogen-rich environments of free-living populations of mice and/or pet store mice. The latter mice more closely resemble humans in terms of immune traits [21]. Rosshart SP et al implanted C57BL/6 embryos into wild mice to produce a new colony of C57BL/6 mice ("wildlings") which retained natural microbiota and pathogens [22]. In spite of this, the low variation and useful attributes described above have made mouse models an invaluable tool for advancing biomedical progress.

Inbred strains, transgenic and congenic mice with inbred backgrounds are commonly used mouse models. An inbred strain is defined as a strain that has been through at least 20 generations of sib-mating (or its equivalent), making animals from the same inbred strain effectively genetically identical. Transgenic mice with particular mutations of interest are relatively simple to produce with modern genetic engineering methods like the injection of targeting vectors or CRISPR. Once produced these mutations of interest frequently must be bred into a congenic line. Congenic strains, which introduce a particular trait or mutation into a predominantly inbred background, are achieved through repeated backcrosses of the mutation of interest into an inbred background strain usually for at least 10 generations.

The most cited mouse strains are C57BL/6, BALB/c, CD-1, SCID, and A/J (Table 4). Only CD-1 is an outbred strain. Below we briefly discuss each of these strains.

C57BL/6 mice, also called "C57 black 6" or simply "Black 6" or abbreviated as 'B6', has the advantages of strain stability and easy breeding. This is also the first mouse strain whose genome was fully sequenced in 2002, soon after the human genome. The International Mouse Phenotyping Consortium IMPC [23], launched in September, 2011, aims to catalog the function of every mouse gene in this strain through knockout technologies.

The use of C57BL/6 mice consists of three main overlapping approaches. First, they frequently serve as physiological or pathological models for in vivo studies. For example, Strickley JD et al investigated mouse immunity to commensal papillomaviruses using C57BL/6 and other mice [24]. Szőnyi A et al used wild-type and transgenic C57Bl/6J mice (ChAT-iRES-Cre, CRH-iRES-Cre, vGAT-iRES-Cre, vGAT-iRES-Cre::Gt(ROSA26)SorCAG/tdTomato ) to study the role of brainstem nucleus incertus GABAergic cells in contextual memory formation [25]. Zott B et al studied the effects of beta-amyloid peptide dimers on the suppression of glutamate reuptake and neuronal hyperactivation in C57BL/6N wild-type mice and Alzheimer's disease models [26]. Also, in 2015, using C57BL/6 mice, researchers discovered central nervous system lymphatic vessels [27]. Second, they are often applied to build transgenic mouse models, such as those with the photoactivatable green fluorescent protein (PA-GFP) [28]. Many such transgenic lines are then used for the in vivo studies just mentioned. Third, C57BL/6 mice are often used as a background strain for the generation of congenics with both spontaneous and induced mutations. However, care must be taken because specific sublines may harbor genetic variants, which may introduce complications in any gene-targeting studies, as reported in the case of C57BL/6NHsd [29].

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Figure 1. Female C57BL/6, 22 months of age.

Due to its popularity several substrains of C57BL/6 have been established. It is important to know with which substrain you are working because important genetic and phenotypic variation exists among them [30]. The common C57BL/6 substrains include C57BL/6J (maintained at The Jackson Laboratory) and C57BL/6N (established at National Institute of Health). IMPC selected embryonic stem cells from C57BL/6N [31, 32], while Mouse Genome Sequencing Consortium [33] and Allen Brain Atlas [34] used C57BL/6J. The substrains have phenotypic differences [35, 36], and some of the underlying genetic variations have been identified [35, 37]. For example, a nonsynonymous mutation of serine to phenylalanine (S968F) in cytoplasmic FMRP interacting protein 2 (Cyfip2), present in the C57BL/6N substrain and not in the B57BL/6J substrain, is responsible for lower acute and sensitized response to cocaine and methamphetamine observed in the substrain [37].

Most C57BL/6 substrains are "genetically ablated of one of the most important mitochondrial antioxidant enzyme, transhydrogenase (gene NNT), due to a natural deletion in the exons of this gene that completely prevents the expression of the protein [35, 38] ", and the mutation is responsible for the impaired glucose clearance and slightly higher resting glucose levels than strains with wild-type Nnt such as C57BL/6NJ [39]. C57BL/6J mice with the Nnt mutation have a normal lifespan, are not diabetic, and have the normal diet-induced obesity response (from Jackson Laboratories).

Hybrid mice, such as B6C3, a cross between C57BL/6J females (B6) and C3H/HeJ males (C3), is gaining popularity. The hybrid mice are heterozygous genetically and tend to serve as a background for some deleterious mutations. Holth JK et al used Jackson Laboratory B6C3F1/J mice (#100010) and B6C3 tau P301S mice (# 008169) to study mouse brain interstitial fluid tau level during the sleep-wake cycle [40].

Among the articles surveyed by Labome, a significant percentage cites the C57BL/6 mouse strain. It is likely that the C57BL/6 strain will continue to be the preferred strain, due to the fact that its genome has been sequenced, to the concerted effort of gene functional analysis by IMPC and other systematic efforts such as connectome construction [41]. While the advantage of using a "standard" strain in research is apparent, interesting issues have been raised about the drawbacks of such a practice, see The Trouble With Black-6.

Wild type, congenic, and transgenic/knockout C57BL/6 mice from The Jackson Laboratory (C57BL/6J) have been used to study, for example, metabolic orchestration of cell death by AMPK-mediated phosphorylation of RIPK1 [42], biomarker discovery for Alzheimer's disease [1], transient microbiota depletion [43], the innate myeloid cell memory to nonself MHC molecules [5], the effect of high salt diets on tau hyperphosphorylation in brain and dementia [44], the induction of transcription factors in neurons by depolarization [45], the role of brainstem nucleus incertus GABAergic cells in contextual memory formation [25], neurogenesis in prostate cancer [46], venous thrombosis and NETosis [47], recipient hosts for adoptive transfer [48], the role of synaptotagmin-3 in endocytosis and synaptic strength [49], alpha-synuclein neurodegeneration in Parkinson’s disease [50]. When crossed with mice having a floxed gene, nestin-Cre transgenic C57BL/6J mice from Jackson laboratory can be used to achieve conditional inactivation of the gene in the nervous system [51]. ROSA26R(EYFP) mice with a background of C57BL/6 are commonly used to indicate the Cre expression [52]. Chopra S et al backcrossed Vav1^cre and CD11c^cre mice with other floxed mice to generate conditional knockouts in leukocytes or dendritic cells, respectively [53]. Rosshart SP et al used SPF C57BL/6 mice from the Jackson Laboratory to study the microbiota and immune responses of laboratory mice born to wild mice [22].

Charles River Laboratories (also its joint venture Vital River in China) is another major supplier of C57BL/6 mice. As with C57BL/6J, Charles River C57BL/6 (C57BL/NCrl) mice have been used to study a wide array of subjects in biology. This has included SOX2-chromatin interaction [54], histone modifications during human parental-to-zygotic transition [55], and cerebrospinal fluid influx during ischemia [3].

C57BL/6 mice from Taconic (C57BL/6NTac) were used to study the innate myeloid cell memory to nonself MHC molecules [5], the microbiota and immune responses of laboratory mice born to wild mice [22], lysosome function and macrophage homeostasis [56], the involvement of rapamycin through mTORC2 disruption in insulin resistance [57] and skin microbiota [58]. Hang S et al studied C57BL/6NTac mice with segmented filamentous bacteria from Taconic Bioscience [59]. Ciccone R et al used Tg2576 mice and WT littermates from Taconic, as an Alzheimer disease model to study neuronal hyperactivity [60].

Harlan Laboratories C57BL/6 mice were used to study the regulatory mechanism of T cell differentiation [61].

Wang L et al purchased C57BL/6 mice from Joint Ventures Sipper BK Experimental Animal in Shanghai, China to study the innate immune response against nuclear viral DNA [62]. Persson EK et al used C57BL/6 mice (6 to 7 weeks old) from Janvier Labs in Saint-Berthevin, France to investigate Charcot-Leyden crystals [63]. B de Laval et al obtained CD45.2 mice from Janvier [64]. Noda S et al transplanted human primary dental pulp stem cells into the calvarial bone cavities of C57BL/6JJcl mice obtained from CLEA Japan [65]. Dominy SS et al obtained specific pathogen–free (SPF) female BALB/c mice from Envigo to study Porphyromonas gingivalis in Alzheimer's disease brains [66]. Moro A et al isolated dermal fibroblasts for 3D fibrin gel assays from Envigo C57BL/6 mice to study the role of microRNA in tissue stiffness hemeostasis [67]. Academic or national animal facilities are also suppliers. C57BL/6J mice of both sexes from the NIA Aged Rodent Colonies were used to study the involvement of L1 retrotransposon during cellular senescence [68].

BALB/c is an albino, immunodeficient inbred mouse strain. BALB/c mice have the characteristics of easy breeding and minimal weight variations between males and females. While BALB/c mice serve as a general purpose animal model, this strain is used extensively for hybridoma and monoclonal antibody production, for example, for the generation of anti-neuropilin-1 antibodies [7], anti-trptase antibodies [69], and others [70], and are especially useful for research in cancer therapy and immunology. It is noteworthy that the mammary tumour incidence in BALB/c mice is low, but they are very sensitive to carcinogens, and can develop lung tumours, reticular neoplasms, renal tumours, and other cancers. In addition, mineral oil injection can readily induce plasmacytomas in BALB/c strain.

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Figure 2. BALB/c mouse. Courtesy of The Jackson Laboratory

Examples of research with BALB/c mice include examination of antiplasmodial immunity in mosquitos [71], demonstrating the host response to influenza A virus is modulated by the novel protein PA-X [72], and studying the effectiveness of antibody CR8020 against group 2 influenza viruses in BALB/c mice from Charles River [73]. Charles River BALB/c mice were used to perform parasite infection to study the antiplasmodial immunity in mosquitos [71].

One common application of BALB/c, as with C57BL/6, is to serve as the background strain for various gene deficiency/knockout studies.

As stated above, BALB/c mice play important roles in oncological research. For example, Mauffrey P et al used Balb/c nu/nu from Charles River laboratories to study neurogenesis in prostate cancer [46]. Besse A et al studied proteasome inhibition in age-matched female Balb/c mice from Charles River to optimize the treatment of multiple myeloma with individual proteasome inhibitors [74]. Yi W et al performed subcutaneous xenografts by using Charles River Laboratories athymic nude (Nu/Nu) mice to show that FGFR-TACC fusion happened in specific GBM patients [75] and studied the role of PFK1 glycosylation in cancer cell growth using Charles River Laboratories nude mice [76]. Kessler JD et al demonstrated that Myc-dependent cancer needs SUMOylation for tumorigenesis by performing breast cancer cell line xenografts using Harlan Labs female athymic nude Foxn1-nu mice [77].

Another commonly used mouse model is the albino CD-1 mouse. While both C57BL/6 and BALB/c mice are strains inbred to establish the genetic homogeneity, CD-1 mice stand out among the most commonly used research mice as an outbred stock (note: inbred mice are referred as strains, whereas outbred mice are referred to as stocks). The genetic variability in such outbred research animal models can be an advantage in the positional cloning of quantitative trait loci and phenotypic or genotypic selection of particular traits. However, the usage of outbred stocks like CD-1, in research fields such as toxicology (safety and efficacy testing), aging, and oncology have been critically assessed and may not be beneficial in many cases [78]. For example, Luther A et al conducted pharmacokinetic, toxicity, in vivo efficacy studies of candidate antibiotics in CD-1 mice [79].

Several publications used CD-1 mice, from Charles River Laboratories [10, 80] or Harlan [9]. Labonté B et al studied the regulatory role of a novle lncRAN MAALIN on impulsive and aggressive behaviours in CD-1 mice [80]. Patzke C et al obtained primary hippocampal or astrocyte culture from newborn CD1 wild type mice from Charles River Laboratories [81].

CB17 SCID mouse (SCID means severe combined immunodeficiency) is an albino strain with a spontaneous SCID mutation. The mutation prevents the development and maturation of both T and B cells. However, SCID mice have normal NK cells, macrophages and granulocytes. They share the same appearance as the normal mice. Due to the SCID mutation, the success ratio of human tumor transplantation is very high (even higher than nude mice), which makes them into a valuable immunodeficient animal model for testing new cancer treatments, for example [11], and as hosts for human immune system tissues.

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Figure 3. SCID mouse. From Dr. Patricia Brown, NCI, NIH.

Eaton JK et al determined the pharmacokinetic properties

of GPX4 protein inhibitor, JKE-1674, in SCID mice from Janvier Laboratories [82].

The A/J mouse is another common albino model, with unique characteristics such as a late-onset progressive muscular dystrophy and adrenal cortical hormone induced congenital cleft palate. It also has a high incidence of spontaneous lung adenomas, which can easily develop in response to carcinogens.

Labome identified 4 publications using A/J mice as animal models (Table 1). Takeda K et al used A/J mice in their study of the role of death receptor 5 mediated-apoptosis in cholestatic liver disease [83]. A/J mice were used by Losick VP et al to investigate the role of a hemidominant Naip5 allele in immunity [84], by Sanders CJ et al to show the role of flagellin in adaptive immunity [85], and by Neunuebel MR et al to investigate SidD modulation of Rab1 de-AMPylation in L. pneumophila infection [86].

ICR mice, also an albino strain, originated in Switzerland and were selected by Dr. Hauschka to create a fertile mouse line. This outbred stock was named after the Institute of Cancer Research in the USA [78, 87]. ICR mice are characterized by docile nature, high productivity, rapid growth rate and a low incidence of spontaneous tumors [88]. Main suppliers of ICR mice are Taconic and Japan SLC. ICR mice are a general-purpose model, used in particular in toxicology, neurobiology, oncology, epidemiology, infection, pharmacology, and also in product safety testing. Nagamatsu G et al obtained embryonic and newborn ovaries from ICR mice to investigate the dormancy of immature oocytes in primordial follicles [89]. Luther A et al tested in vivo tolerability of candidate antibiotics in ICR mice [79].

Other mouse strains such as FVB/N mice from Charles River [24, 90], PWK/PhJ from Jackson Laboratory [55], NMRI nude mice [91] and Swiss Webster (SW) mice [92, 93], are also used in biomedical research.

Genetically-defined and genetically-modified mice (and rats) are widely used in research to investigate the function of specific genes, and to serve as experimental models for different human disease. Thousands of such strains are available, with a myriad of gene alterations, strain selections, and potential applications. Also extensively used are mice with other gene alterations, such as fluorescent reporter mouse lines [94, 95].

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Figure 4. Lepr(db-3J) and normal mouse. Lepr(db-3J) mice are "obese, hyperphagic, cold intolerant, insulin resistant, and infertile". Courtesy of The Jackson Laboratory

Differences exist among the various mouse models and it is important to be aware of this variation. For example, the behavioral difference among mouse strains/stocks is common. C57BL/6 and Swiss Webster mice had different levels of sociability [96] and responded differently to severe spinal cord injury [97]. Dizocilpine maleate (MK-801) showed differential effects on cerebrocortical neuronal injury in C57BL/6J, NSA, and ICR mice [98]. Significant performance differences between two related outbred albino stocks of mice, ICR and CD1, were observed in cognitive tasks. ICR suffers from a severe visual impairment making this stock difficult to use in the Morris water maze that requires good visual perception. CD1 does not suffer from grossly impaired vision but, similarly to the ICR strain, CD1 mice exhibit decreased freezing in all phases of context-dependent fear conditioning [99]. In addition, ICR mice from different sources may give rise to different, even contradictory research results [100].

Another rodent, the rat (Rattus norvegicus), is the second most cited animal model used in biomedical research. Compared to mice, rats are bigger, generally more aggressive, and more resistant to various ailments. Sprague-Dawley and Wistar are the two most frequently used rat models. Similar to most common mouse models, these two rat strains are albino. On the other hand, both rat models are outbred stocks while the most commonly used mice are inbred strains.

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Figure 5. Sprague-Dawley rat. Courtesy of Harlan Laboratories

The Sprague-Dawley rat is a hybrid albino strain with a long narrow head. It has a high reproductive rate and low incidence of spontaneous tumors. Its calm temperament and easy handling are welcome features to both scientists and animal lab technicians. Most of publications Labome surveyed using Sprague-Dawley rats as animal models were from Charles River, for example, [101].

Sprague-Dawley rats are used extensively in neurobiological research. Brigidi GS et al isolated hippocampal neuronal cells from P0 Sprague–Dawley rats from Charles River [45].

The pathological investigation is another area that Sprague-Dawley rats are frequently utilized. Lundby A et al injected epidermal growth factor into Sprague-Dawley rats from Charles River to study tyrosine phosphorylation in lungs [102].

Wistar rat is another common hybrid albino model animal. It has the distinct honor of being the first rat stock developed to serve as a model animal. The substrains of Wistar rats: Wistar Hannover (Han/Wistart) and Wistar Unilever (WU) rat are outbred; while Wistar Kyoto and Wistar Furth are inbred strains. Sprague-Dawley rats were derived from Wistar rat.

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Figure 6. Lobund-Wistar rat. From NCI, NIH.

MC Silva et al investigated CNS penetration of an ATP-competitive mTOR kinase inhibitor AZD2014 in Han Wistar male rats purchased from Vital River [103]. Eaton JK et al isolated hepatocytes from Han/Wistar rats to characterize the pharmacokinetic properties of GPX4 inhibitors [82]. Duncan A et al obtained Wistar rats from Charles River to study the role of habenular TCF7L2 in connecting nicotine addiction to diabetes [16].

The Jackson Laboratory, founded by Clarence Cook Little, who produced the inbred mouse strain C57BL, among others, is the most cited experimental murine animal supplier. More than 11,000 strains of mice are available from The Jackson Laboratory. It also maintains an integrated mouse information resource. It distributed 3.0 million mice to more than 1900 institutions in 75 countries (The Jackson Laboratory website).

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Figure 7. The Jackson Laboratory

The Jackson Laboratory is the primary source for common mouse strains like C57BL, BALB/c mouse strains, and rat strains, and less common strains like FvB/NJ [104], and 129 X1/SvJ [73].

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Figure 8. DBA/2J mouse. Courtesy of The Jackson Laboratory

In addition, many of congenic and transgenic mouse strains also came from The Jackson Laboratory, such as hAPP-J20 [105], Nlrp3−/− and Casp1−/− [106], APP/PS1 mice [107], NSG mice (NOD-SCID-IL2R gamma chain-deficient [6, 108, 109], Rag1-/- [110], Down syndrome model Ts65Dn [111], lineage-tracing R26YFP [112], Rag2-/- [113], Xpc−/− and Cd8−/− [24], Rosa26LSL-spCas9-eGFP (026175), ChAT-Cre (006410), ChATDW167 TRAP (030250), BAT-GAL (00531) and ROSA-tdTom (007914) [16], NSG-SGM3 mice [69], fluorescent reporter lines Rosa26 LSL-N1ICD-IRES-nEGFP, Rosa26LSL-ZsGreen (Ai6), Rosa26LSL-tdTomato (Ai9) [94], Ai9 and Ai96 reporter mouse lines [95], Apoe−/− mice [114], TLR2−/−, mtCATtg, and Duox2−/− mice [115], Syt3 and Syt6 knock-out and Syt5 and Syt10 knock-in quadruple targeted mutation mice (stock no. 008413) [49].

Charles River has been providing research animals for more than 70 years. It is a supplier of both mouse and rat models, as well as other mammalian models. It is an important supplier for common strains like NIH-Foxn1rnu nude rats [116], Rag1−/− [117], FVB [24], C57BL [49, 117], BALB/c [46, 117], and other strains like Swiss-Webster mice [93], NMRI nude mice [91]. In addition, it provided most CD-1 mice and rat stocks, for example, timed pregnant Sprague Dawley [14] and regular Sprague Dawley [116], Long Evans [118] and Wistar [16], among the publications surveyed.

Taconic Biosciences has been providing genetically-defined rats and mice for 60 years. In addition to the common strains like C57BL, Taconic provided or generated Plg−/− mice [2], Tg2576 mice [105], LysMgfp/gfp mice [119], 129S6.Cg-Tg(APPSWE)2576Kha N20+ mice [44], germ-free Swiss Webster mice [120] and Long Evans rats [17].

Its famed breeding facility, Sprague-Dawley farm in Madison, Wisconsin, where the namesake rat strain, Sprague Dawley rat, was initially bred, is now part of Harlan. Harlan supplies Hsd nude mice [121], Dark Agouti rat [122], C57BL mice [61], FVB mouse [123], athymic nude Foxn1-nu mouse [77], and SJL/J mice [124].

Other suppliers include government agencies such as the NCI Mouse Repository [125] and RIKEN BioResource Research Center [3], organizations like DKFZ animal facility [91], UC Davis Mutant Mouse Resource & Research Center [117, 126], University of Alabama at Birmingham (UAB) animal facility [127], Frederick Cancer Center / National Cancer Institute, NIH [46, 127], and commercial suppliers like Shanghai Model Organisms [42], Animal

Resources Centre [6], Janvier Laboratories [82] (NOD-SCID [106] ), Envigo [66, 67, 128], Japan Shimizu Laboratory Supplies [17] and SLC [15, 89]. Companies such as GenOway (human VISTA knockin mice [117] ) can also generate transgenic animals on demand.

IMSR is a collaboration of a dozen international mouse repositories, containing information for 56,886 strains and 231,033 EC cell lines as of September 2019. For example, here are 130 strains for mouse p53 gene. The website is supported by an NIH grant.