ANIMAL MODEL FOR HIV-1 INFECTED HUMAN MICROBIOTA
EXPLORATORY MICROBIOME STUDY
Bella Malherbe
ABSTRACT
Within this project, the microbiome of Fischer rats, C57 mice, and deer is explored in relation to previous research done on HIV-1 microbiota to determine which of the models’ microbiota best emulates those conditions. Fecal pellets from these rodents were taken using sterile forceps. The DNA from the fecal pellets was extracted and tested for purity. This purified DNA was then sent to Novagene for amplification, sequencing, and statistical analysis. On average, 1167 of OTUs were identified per individual. The ten most abundant phyla of bacteria found within all of the animals were Lentisphaerae, Deferribacteres, Cyanobacteria, Verrucomicrobia, Tenericutes, Actinobacteria, Proteobacteria, Spirochaetes, Bacteroidetes, and Firmicutes.The Fisher rats and C57 mice also demonstrate the increased relative abundance of Proteobacteria that has been demonstrated to have occured in HIV-1 gut microbiomes (Dillon et al., 2014).Within the HIV-1 gut microbiome is a chao1 index of 67.0 and a shannon diversity of 3.4 (Dillon et al., 2014). The most comparable alpha indexes are the C57 mice because they have the lowest amount of diversity within their microbiomes with an average shannon diversity of 6.988 and a chao1 index of 1037.493. Overall, C57 mice demonstrated the closest relative abundance of bacterial species and species richness to the HIV-1 microbiota. However, more research is needed to increase the understanding of model microbiota and the microbiota of HIV-1 to create the best possible environment for research.
BACKGROUND
HIV
Human immunodeficiency virus (HIV) is a retrovirus that causes the progressive and substantial loss of host helper T cells (Th). Primarily, HIV-1 has a tropism for the host’s CD4+ Th cells which causes a degradation of the ability to fight infection. With recent research it has been found that HIV-1 is chiefly a mucosal disease that will manifest itself systemically (McHardy et al. Microbiome 2013)Disregarding the route of viral infection, it is clear that HIV-1 infections cause the majority of their damage to gut associated lymphoid tissue (GALT) (Brenchely et al., 2004). Because of its acute involvement in the progression of AIDS, the understanding of the GALT’s impairment is essential to the comprehension of the disease as a whole
GUT MICROBIOME
The gastrointestinal tract is a hub for commensal bacteria.It is estimated that the human colon alone has a bacterial concentration of about 1000000000000 cells (Sender et al., 2016). This massive population of bacteria, along with the bacteria on the rest of the human body, has been dubbed the microbiome by researchers and has piqued the interest of many scientific institutions. In extended analysis of the average human microbiota it has been observed that the Firmicutes and Bacteroidetes phyla constitute the majority of the dominant healthy human microbiome with Bacteriodetes coming in slightly ahead (Arumugam et al., 2011). The primary families of bacteria found within the gut were shown to be Bacteroidaceae, Clostridiaceae, Prevotellaceae, Eubacteriaceae, Ruminococcaceae, Bilfiobacteriacae, Lactobacillaceae, Enterobacteriaceae, Saccharomycetaceae, and Methanobacteriaceae
IMMUNE SYSTEM
The immune system within the intestines has been found to be phylogenetically ancient; many scientists have hypothesized that its development began even before some of the most basal lymphoid structures, including the thymus (Mueller et al., 2006). Along with its early development, the mucosal immune system is extremely large; up to 70% of all lymphocytes in the human body can be found within the gastrointestinal tract (Mueller et al., 2006).
CONNECTIONS
In recent research it has been found that there is a strong correlation to microbiota composition and the functionality of the mucosal immune system (Abt et al., 2013) system, the commensal microbiome composition can be drastically affected in the presence of viral disease. A statistically significant alteration of microbiota in GALT has been seen to occur in HIV-1 infection by various recent studies (Lozupone et al., 2013). Though the three most dominant phyla, Firmicutes, Bacteroides, and Proteobacteria, remain most dominant in both infected and control individuals, it has been observed that there is a significant loss of species richness, which is positively correlated with a healthy immune system, in HIV-1 infected individuals (Mutlu et al.,2014). Specifically, the microbiome in HIV-infected patients frequently contains higher colonizations of Prevotella, which is associated with many inflammatory disease states such as periodontal disease and active ulcerative colitis, as well as a lower colonization of Firmicutes (Dillon et al., 2014).
METHODS
Animals
Female Rattis norvegicus (Fischer rats), Peromyscus maniculatus (deer mice), and Mus musculus (C57/B6-2) were obtained from established colonies at UNCO. They were housed throughout the duration of the collection period in BSL-2 OptiMICE racks that had ventilation through HEPA filters in the UNCO animal facilities with Harlan Tekiad lab-grade sani chip. In each cage, there was an average of two animals. They were fed 16% protein rodent diets (Teklad Global Diets, Envigo 2016) ad libitum and were supplied with a 200 mL water container. In the facilities, the animals were kept under a 12-hour light: dark cycle (07:00 to 19:00). Upon collection, Rattis norvegicus were an average of 14.5 weeks old, Peromyscus maniculatus were an average of 19.5 weeks old, and Mus musculus were an average of 7 weeks old.
Samples
One freshly evacuated fecal pellet was extricated from four individuals of each species using sterile forceps and directly placed into an empty 2 mL round bottom tube. The samples were then massed and put through the DNA purification process. The DNA was purified using a DNeasy® PowerSoil® Kit (Quiagen). Each lot of these kits are tested against predetermined specifications to ensure consistent product quality. This kit contains 100 MB spin columns, 100 garnet PowerBead tubes, 6.6 mL of solution C1 (sample prep buffer), 30 mL of solution of C2 (lysis), 30 mL of solution C3 (inhibitor remover), 144 mL of solution C4 (inhibitor and salt solution), 60 mL of solution C5 (wash buffer), and 18 mL of solution C6 (elution buffer). It uses a humic substance/brown color removal system. In this kit, samples are added to a bead beating tube for rapid and thorough homogenization. Then, cell lysis occurs through chemical and physical means and total genomic DNA is captured on a silica membrane in a spin column. The DNA is then washed and eluted from the membrane and is thereby considered ready for polymerase chain reaction (PCR) and downstream applications. The purity and concentration of the DNA samples was assessed prior to sample shipping using a NanoDrop™ 2000/2000c spectrophotometer (Thermo Fisher, U.S.A)
16S rRNA Amplification, Sequencing, and Library Preparation
The purified DNA was then sent to Novogene to be sequenced. They ensure that products from each step are evaluated with rigorous criteria of quality. The benchtop workflow of the process is illustrated above (Fig. 1). Within this process, quality control (QC) entails the analysis of purity, integrity, concentration, and size of DNA through 1% agarose gel electrophoresis under voltage of 100V for 40min. PCR amplicons are then examined through 2% agarose gel electrophoresis under a voltage of 80V for 40min. The targeted genes are the bacterial 16S, regions V3 and V4. This was amplified using primers 341F and 806R. All of the PCR reactions performed by Novogene were done with Phusion® High-Fidelity PCR Master Mix (New England Biolabs, U.S.A). The PCR reactions were qualified and quantified by performing gel electrophoresis using 2% agarose gel on equal amounts of PCR products and 1X SYBR green. The company chose samples that contained a bright main strip between 400bp and 450bp (base pairs) for further experimentation. All of the PCR products yielded were mixed in an equidensity ratio and purified with a Qiagen Gel Extraction Kit (Qiagen, Germany). Library preparation was conducted by Novogene using Ion XpressTM Plus Fragment Library Kit (Thermo Fisher, U.S.A). The sequencing strategy used by Novogene is IonS5™XL (Thermo Fisher, U.S.A). This utilizes a semiconductor chip that is covered with millions of wells. Each well contains a bead on which millions of DNA fragments attach. Each well is flooded with one of the four nucleotide bases. Whenever one of these bases attach, a hydrogen ion is released. The number of hydrogen ions released can be measured via a pH that has been translated into voltage. This process applies single end 600 (SE600) and it exceeds at least 200bp over the target length. The QC and delivery of raw data in FASTQ formatting should trim and filter redundant reads as shown in the flowchart below.
DISCUSSION
Within the phylum level, a comparable relative abundance of Firmicutes can be seen between HIV-1 patient microbiota and the C57 mice microbiota. The Fisher rats and the C57 mice also demonstrate the increased relative abundance of Proteobacteria that has been demonstrated to have occurred in HIV-1 gut microbiomes (Dillon et al., 2014). This increased proteobacterium is important in a model because the phylum contains a wide variety of pathogenic bacteria. The increase in this pathogenic bacteria may play an important role in the pathogenesis of HIV-1 and the metabolism of antiretroviral diseases such as HAART. t the genus level none of the models examined show the marked change in the relative abundance of the gram negative anaerobe Prevotella. They also don’t show the lower population size of Bacteroides relative to the population of Prevotella that has been seen in other studies (Dillon et al., 2014). This has been observed to be a key piece in the microbiota’s involvement in the progression of HIV-1. The Prevotella genera of bacteria has been seen to have the ability to function as a pathobiont and alterations of the relative abundance of Prevotella in the gut microbiome has been shown to occur frequently in many inflammatory disease states (Lucke et al., 2006). However, out of all of the potential models, the deer mice have the least relative abundance of Bacteroides and the rats have the most. This may point to the deer mice as a superior model for HIV-1 infected people compared to the other two models examined in the study. Another factor that was compared to data on the HIV-1 infected human gut microbiome data is the species richness of the gut microbiomes. Within the HIV-1 gut microbiome is a chao1 index of 67.0 and a Shannon diversity of 3.4 (Dillon et al., 2014). The most comparable alpha indexes are the C57 mice because they have the lowest amount of diversity within their microbiomes with an average Shannon diversity of 6.988 and a chao1 index of 1037.493. This component could potentially contribute to the overall functionality of the model in HIV-1 drug trials because species richness can greatly affect the overall ability of the microbiome to act symbiotically with the immune system. Overall, the model that complies with the most important aspects of the HIV-1 microbiota is the C57 mice. Because of their comparable phyla relative abundance in relation to HIV-1 infected humans, low diversity, and relatively low amounts of Bacteroides their microbiome contains will most likely function similarly to the way HIV-1 infected individuals might behave. However, C57 mice’s gut microbiota does not perfectly match the gut microbiota typical of an HIV-1 infected human. Further exploration of other models and their gut microbiota is needed to become more confident in the models used to test drug trials with this disease.
BELLA MALHERBE
Bella is interested in virology and microbiology. She plans to get a BS in microbiology and then go on to obtain an MD/PhD and practice infectious disease while researching HIV-1.
ACKNOWLEDGEMENTS
I could have never completed this project without the support of all of these people.
ZIMMERLE FAMILY
Thank you so much to the entire Zimmerle family for providing me with the scholarship so I could have the chance to attend this camp. This has truly been one of the best experiences of my life and I'm sure that it will change the course of the rest of my life. I will be eternally grateful to your family for allowing me to have this experience.
TYLER SHERMAN AND REBA ZIMMERLE
Thank you so much to my mentors who were both absolutely fantastic teachers and role models. I really appreciate your patience with my millions of questions and all of your help editing and perfecting my project. The two of you have really solidified my interest in going into research in the future. Thank you for inspiring me and fostering my learning; I will keep my experience with the two of you close to my heart forever.
FSI STAFF
Thank you to all of the staff at FSI for enhancing my entire learning experience. I am so happy that I got the chance to be a part of this camp that all of you worked to put together and I'm so thankful for all of your hard work.
RESEARCH PARTNERS
Thank you to my research partners Natalie, Sakthi, and Cynthia for being absolutely fantastic teammates. I am really thankful that I got to share my research experience with the three of you.
FRIENDS AND FAMILY
Thank you to my parents for paying for me to attend this camp and supporting my academic endeavors. I love you guys so much. Thank you to all of my friends, both the ones I made here and the ones supporting me from afar. Your support really helped me get here and I am so thankful for that.
REFERENCES
Abt, M. C., Osborne, L. C., Monticelli, L. A., Doering, T. A., Alenghat, T., Sonnenberg, G. F., …
Artis, D. (2012). Commensal bacteria calibrate the activation threshold of innate antiviral
immunity. Immunity, 37(1), 158–170. doi:10.1016/j.immuni.2012.04.011
Abt, M. C., & Artis, D. (2013). The dynamic influence of commensal bacteria on the immune
response to pathogens. Current opinion in microbiology, 16(1), 4–9.
doi:10.1016/j.mib.2012.12.002
Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D. R., … Bork, P.
(2011). Enterotypes of the human gut microbiome. Nature, 473(7346), 174–180.
doi:10.1038/nature09944
Brenchley, J. M., Schacker, T. W., Ruff, L. E., Price, D. A., Taylor, J. H., Beilman, G. J., …
Douek, D. C. (2004). CD4+ T cell depletion during all stages of HIV disease occurs
predominantly in the gastrointestinal tract. The Journal of experimental medicine, 200(6), 749–759. doi:10.1084/jem.20040874
Dillon, S. M., Lee, E. J., Kotter, C. V., Austin, G. L., Dong, Z., Hecht, D. K., … Wilson, C. C.
(2014). An altered intestinal mucosal microbiome in HIV-1 infection is associated with mucosal and systemic immune activation and endotoxemia. Mucosal immunology, 7(4), 983–994. doi:10.1038/mi.2013.116
Gori, A., Tincati, C., Rizzardini, G., Torti, C., Quirino, T., Haarman, M., … Clerici, M. (2008).
Early impairment of gut function and gut flora supporting a role for alteration of
gastrointestinal mucosa in human immunodeficiency virus pathogenesis. Journal of clinical microbiology, 46(2), 757–758. doi:10.1128/JCM.01729-07
Kamada, N., Chen, G. Y., Inohara, N., & Núñez, G. (2013). Control of pathogens and
pathobionts by the gut microbiota. Nature immunology, 14(7), 685–690. doi:10.1038/ni.2608
Kondelková, Katerina & Vokurková, Doris & Krejsek, Jan & Borska, Lenka & Fiala, Zdenĕk &
Ctirad, Andrýs. (2010). Regulatory T cells (Treg) and Their Roles in Immune System with Respect to Immunopathological Disorders. Acta medica (Hradec Králové) / Universitas Carolina, Facultas Medica Hradec Králové. 53. 73-7. doi: 10.14712/18059694.2016.63.
Loyd-Price J., Abu-Ali G., Huttenhower C. (2016). The Healthy Human Microbiome. Genome
Medicine. 8. 51-73. doi: https://doi.org/10.1186/s13073-016-0307-y
Lozupone, C. A., Li, M., Campbell, T. B., Flores, S. C., Linderman, D., Gebert, M. J., … Palmer,
B. E. (2013). Alterations in the gut microbiota associated with HIV-1 infection. Cell host
& microbe, 14(3), 329–339. doi:10.1016/j.chom.2013.08.006
Lucke, K., Miehlke, S., Jacobs, E. & Schuppler,M. Prevalence of Bacteroides
and Prevotella spp. in ulcerative colitis. (2006) J. Med. Microbiol. 55, 617–624 .
Mandl, J. N., Ahmed, R., Barreiro, L. B., Daszak, P., Epstein, J. H., Virgin, H. W., & Feinberg,
M. B. (2015). Reservoir host immune responses to emerging zoonotic viruses. Cell, 160(1-2), 20–35. doi:10.1016/j.cell.2014.12.003
McHardy I.H., Li X., Tong M., Ruegger P., Jacobs J., Borneman J., Anton P., Braun J. (2013).
HIV Infection is Associated with Compositional and Functional Shifts in the Rectal
Mucosal Microbiota. Microbiome. 1. 1-12. doi: https://doi.org/10.1186/2049-2618-1-26
Merlini, E., Bai, F., Bellistrì, G. M., Tincati, C., d'Arminio Monforte, A., & Marchetti, G. (2011).
Evidence for polymicrobic flora translocating in peripheral blood of HIV-infected patients with poor immune response to antiretroviral therapy. PloS one, 6(4), e18580. doi:10.1371/journal.pone.0018580
M. Kabat, Agnieszka & Srinivasan, Naren & J. Maloy, Kevin. (2014). Modulation of immune
development and function by intestinal microbiota. Trends in immunology. 35. doi: 10.1016/j.it.2014.07.010.
Momose, Yoshika & Hirayama, Kazuhiro & Itoh, Kikuji. (2008). Competition for proline
between indigenous Escherichia coli and E. coli O157:H7 in gnotobiotic mice associated with infant intestinal microbiota and its contribution to the colonization resistance against E. coli O157:H7.Cell host & microbe, 10(4), 311–323. doi:10.1016/j.chom.2011.10.004
Mueller, C., & Macpherson, A. J. (2006). Layers of mutualism with commensal bacteria protect
us from intestinal inflammation. Gut, 55(2), 276–284. doi:10.1136/gut.2004.054098
Mutlu, E. A., Keshavarzian, A., Losurdo, J., Swanson, G., Siewe, B., Forsyth, C., … Landay, A.
(2014). A compositional look at the human gastrointestinal microbiome and immune activation parameters in HIV infected subjects. PLoS pathogens, 10(2), e1003829. doi:10.1371/journal.ppat.1003829
Pandiyan, Pushpa & Bhaskaran, Natarajan & Zou, Mangge & Schneider, Elizabeth & Jayaraman,
Sangeetha & Huehn, Jochen. (2019). Microbiome Dependent Regulation of Tregs and
Th17 Cells in Mucosa. Frontiers in Immunology. 10. 426. doi: 10.3389/fimmu.2019.00426.
Rocafort M., Noguara-Julian M., Rivera J., Pastor L., Gullien Y., Langhorst J., Parera M., …
Paredes R. (2019). Evolution of the Gut Microbiome Following Acute HIV-1 Infection. Microbiome. doi: 10.1186/s40168-019-0687-5
Roghanian A. (2014). Dendritic Cells. Retrieved from
https://www.immunology.org/public-information/bitesized-immunology/células/dendritic-cells
Sankaran, S., George, M. D., Reay, E., Guadalupe, M., Flamm, J., Prindiville, T., & Dandekar, S.
(2008). Rapid onset of intestinal epithelial barrier dysfunction in primary humanimmunodeficiency virus infection is driven by an imbalance between immune response and mucosal repair and regeneration. Journal of virology, 82(1), 538–545. doi:10.1128/JVI.01449-07
Sender, R., Fuchs, S., & Milo, R. (2016). Revised Estimates for the Number of Human and
Bacteria Cells in the Body. PLoS biology, 14(8), e1002533. doi:10.1371/journal.pbio.1002533
Tesmer, L. A., Lundy, S. K., Sarkar, S., & Fox, D. A. (2008). Th17 cells in human disease.
Immunological reviews, 223, 87–113. doi:10.1111/j.1600-065X.2008.00628.x
Vujkovic-Cvijin, I., Dunham, R. M., Iwai, S., Maher, M. C., Albright, R. G., Broadhurst, M. J.,
… McCune, J. M. (2013). Dysbiosis of the gut microbiota is associated with HIV disease progression and tryptophan catabolism. Science translational medicine, 5(193), 193ra91. doi:10.1126/scitranslmed.3006438
Zhu J., Paul W. E. (2008). CD4 T cells: fates, functions, and faults. Blood. 112(5). 1557-1569.
