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Effect of antibiotics on the gastrointestinal microbiome





Stage 1: Introduction

Antibiotics significantly impact the gut microbiome and overall health of the animals. This research aims to underpin the effect of antibiotics on the gastrointestinal microbiome of the koalas with Chlamydia. Antibiotics are known to improve Chlamydia infections (Phillips et al. 2018). Chlamydia infections are sexually transmitted and found in humans. The Chlamydia infections have also hit the koalas with certain populations being affected with 100% infection rate. Antibiotics are often used for the treatment of Chlamydia using antibiotics azithromycin and doxycycline. The disease is caused by a bacterial infection Chlamydia trachomatis (Legione et al. 2016). In koalas, the infection has emerged as an epidemic and is also transmitted by pap consumption in baby koalas. However, the use of antibiotics is also associated with the changes in the gut microbiome. The antibiotics impact the host immunity by altering the bacterial metabolites and change how cellular signalling occurs via the gut microbiota (Robbins et al. 2018). The antibiotic medication is given for the treatment of Chlamydia also kills the bacteria present in the gut microbiota that is considered to be beneficial for the bacteria and aids in the digestion. Therefore, this treatment results in alteration of nutrition in the diet of the koala bears bears (Dahlhausen et al. 2018). This proposal aims to highlight the impact of the antibiotics on the gut microbiota of the koalas that have Chlamydia infections.


To see how antibiotics affects the gastrointestinal (GI) microbiome of the koalas with Chlamydia


If antibiotics and food supplements are introduced to a koala's GI microbiome, there will be changes in the koala’s metabolism visible by change in the body mass

Study species

  • Phascolarctos cinereus more commonly known as Koala is a native Australian arboreal marsupial. They live in a woodlane and semi-arid communities dominated by their specific diet, Eucalypt trees.
  • Populations will be sampled from captive koalas from Port Macquarie Koala Hospital.


Stage 2: Methodology

Type of experiment

  • Manipulative research.
  • This experiment will be conducted in the Port Macquarie Hospital where captive koalas are being treated for chlamydia = conducted in a field (hospital setting)
  • Comparison of the impact of antibiotics on the deteriorating health of Chlamydia affected koalas
  • This experiment is conducted in between groups.

Experimental design principles

5 replicates in each treatment group as well as control - random allocation in each group. Five replicates have been chosen to observe the concordance in the results and make the study more significant.Koalas are rescued from the national parks, mostly from NSW and a few from Victoria. - we believe that because the koalas are not from the same area, that this would not be describing pseudoreplication.

Experimental design elements


  • Negative control:  15 koalas w/ diet (manna gum)
  • 2 Treatment group: 15 koalas w/ diet (manna gum) + antibiotic (oxytetracycline and penicillin)

Confounding factors:

  • Diet = give the same food.
  • Stage of chlamydia in koalas: pick koalas that have the same symptoms: blindness and urinary tract infection (wet bottoms)
  • Age = koalas on the age of 10-15 years



Body weight of the animals: Body weight is an indication of the effectiveness of the gut microflora, which means that we can look at body mass as an indication if antibiotics had an impact in the GI microbiome


  1. Body weights measured at the start of the experiment
  2. Koalas are fed everyday, and antibiotic treatment (tablet) as well as supplement is administered daily.
  3. Body weights measured weekly (end of week) for the course of ten weeks.
  4. Same weighing scales measured. Same person recording measurements.
  5. Collection of feces for the assessment of gut microflora

Statistical test

There is one independent variable: type of treatment, and four groups within it (Control and Treatments 1 to 3. So one-way ANOVA or the Kruskal Wallis test would be done.

Stage 3: Conclusion

Chlamydia is spreading in the Koala population as an epidemic. Even when antibiotics are commonly prescribed for the treatment of the infection, the antibiotic consumption is associated with changing the gut microbiota in the koalas. This research will serve as evidence of the changing gut microflora due to antibiotic consumption prescribed for the treatment of chlamydia infections through the assessment of biomass.


Dahlhausen, K.E., Doroud, L., Firl, A.J., Polkinghorne, A. and Eisen, J.A. 2018. Characterization of shifts of koala (Phascolarctos cinereus) intestinal microbial communities associated with antibiotic treatment. PeerJournal, 6, p.4452.

Legione, A.R., Patterson, J.L., Whiteley, P.L., Amery-Gale, J., Lynch, M., Haynes, L., Gilkerson, J.R., Polkinghorne, A., Devlin, J.M. and Sansom, F.M.  2016. Identification of unusual Chlamydia pecorum genotypes in Victorian koalas (Phascolarctos cinereus) and clinical variables associated with infection. Journal of Medical Microbiology, 65(5), pp.420-428.

Phillips, S., Robbins, A., Loader, J., Hanger, J., Booth, R., Jelocnik, M., Polkinghorne, A. and Timms, P. 2018. Chlamydia pecorum gastrointestinal tract infection associations with urogenital tract infections in the koala (Phascolarctos cinereus). PloS one, 13(11).

Robbins, A., Loader, J., Timms, P. and Hanger, J., 2018. Optimising the short and long-term clinical outcomes for koalas (Phascolarctos cinereus) during treatment for chlamydial infection and disease. PloS One, 13(12).


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