Why some Lactobacilli aren’t who they seem

Author: Dr Ken McGrath

19 December 2019



Lactobacillus is frequently reported in stool samples that are analysed using culture and 16SrRNA-based tests, so why does metagenomics detect it far more rarely in Australian gut microbiomes?

This simple confusion comes down to a misidentification in 1974 which has yet to be corrected, despite several calls for it to be amended. In 1974, an organism that should be called Lachnospira rogosae was incorrectly characterised and named as a Lactobacillus species because it looked similar when grown in cell culture1. However, it was a different class of organism – more unrelated than genus, family and order – and performing functions in the gut that are quite different to that of Lactobacillus.

Why does this affect Lactobacillus prevalence?

Despite many researchers recognising and calling out this error, this mistake in identification has been carried forward into the modern genetic databases that many 16S-based testing providers use.  Researchers have requested this mistake be rectified and the databases updated, with scientists first requesting the change to be made in 20042 and again in 20143. Others have more recently noted that the misclassified organism “may therefore not belong to the genus Lactobacillus4” and should be renamed correctly to Lachnospira rogosae.

Because metagenomics-based testing looks at the whole genomes of organisms, it is able to pick up these differences and correctly identify the organisms present in a sample. These findings are in line with other studies that show Lactobacillus does not typically colonise in the adult human lower gut5, and that it should rarely be seen using modern testing methods.

Metagenomics gut microbiome

Find out more about what metagenomics can tell you, with Dr Ken McGrath’s “How does Metagenomics work? Solving the puzzle of your gut microbiome” blog.  Discover more.

What does this mean in clinical practice?

If you are utilising culture/CDSA or 16S-based tests, then there is a high likelihood that Lachnospira rogosae will be incorrectly identified and reported as Lactobacillus. According to Microba’s analysis of a subset of their testing group (n=3,093), Lachnospira rogosae is present in around 35% of Australian gut microbiomes, whereas Lactobacilli are only detected in less than 3%. This means that the abundance and prevalence of Lactobacillus is likely being over-estimated in Comprehensive Digestive Stool Analysis (CDSA) and 16S-based tests.

It is important when treating a patient based on CDSA or 16S-based tests that the practitioner recognises that any clinical action taken from the detection of Lactobacillus may be misinformed. Understanding the difference between the two is key to clinical practice and ensuring a patient receives the correct treatment. Lactobacilli tend to perform beneficial functions in the gut, while Microba’s analysis of the Lachnospira rogosae genome show it can produce branched-chain amino acids, which have been linked to type-2 diabetes.

How can I ensure my patients’ results are correct?

Health care practitioners are passionate about their patients receiving the most accurate treatment to assist in recovery and long-term health goals. In order to ensure that your patient has access to the most detailed, accurate gut microbiome analysis service, look towards metagenomics.

Metagenomics – such as the method Microba uses – looks at the whole genome to identify which species are in a stool sample, as well as their metabolic functions. When combined with a modern genome-based database, this will mean that if Lachnospira rogosae is present in the sample, it is correctly identified and reported in the complete microbiome profile. It will also include a description indicating that the organism was previously known by another name in outdated systems.

With metagenomics providing the whole picture of a patient’s gut microbiome, including all species detected and their metabolic functional capacity, correct clinical interpretation is enabled. You can be confident that the best standards of practice are undertaken with this high-resolution metagenomics profile, and you are using the right information in your patient management.

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About the Author

Dr McGrath is the Clinical Liaison Manager with Microba. He has a PhD in Molecular Pathology from the University of Queensland, with a research background in microbial community genomics, including human and environmental microbiomes and metagenomics analysis. Ken has also been a part of several international microbiome research projects.


1.Holdeman, L. V. & Moore, W.E.C. (1974). New Genus, Coprococcus, Twelve New Species, and Emended Descriptions of Four Previously Described Species of Bacteria from Human Feces. International Journal of Systematic and Evolutionary Microbiology, Vol. 24, Issue 2. https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/00207713-24-2-260

2.Felis, G.E., Torriani, S. & Dellaglio, F. (2004). The status of the species Lactobacillus rogosae Holdeman and Moore 1974. Request for an Opinion. International Journal of Systematic and Evolutionary Microbiology, Vol. 54, Issue 5. https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijs.0.63099-0

3.Tindall, B.J. (2014). The status of the name Lactobacillus rogosae Holdeman and Moore 1974. Opinion 88.Judicial Commission of the International Committee on Systematics of Prokaryotes. International Journal of Systematic and Evolutionary Microbiology, Vol. 64, Issue 10. https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijs.0.069146-0

4.Miyake, S., Kim, S., Suda, W., Oshima, K., Nakamura, M., Matsuoka, T., Chihara, N., Tomita, A., Sato, W., Kim, S., Morita, H., Hattori, M. & Yamamura, T. (2015). Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters. PLoS ONE 10(9):e0137429. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0137429

5.Walter, J. (2008). Ecological Role of Lactobacilli in the Gastrointestinal Tract: Implications for Fundamental and Biomedical Research. Applied and Environmental Microbiology, August; 74(16): 4985-4996. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2519286/