The Latest Science on Microbiome Testing
How useful is microbiome testing? What are the benefits and limitations? What can it tell me? How much do we know about our microbiomes? What is the best gut test?
Limitations:
Current limitations and unknowns are extreme. There are a plethora of microbes which are either unknown and/or not tested for currently. 16s only tests for bacteria, and not down to the strain level, which is of vital importance.
This recent study for example, showing one bacterial strain inducing liver damage (2018): http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0198262 - That kind of thing is absolutely not tested for with either conventional, or 16s commercial testing.
Till mid 2016 they were only able to culture an estimated 1% of gut microbes: https://archive.is/JnStd – https://www.nature.com/articles/nature17645
Only 35 to 65% of molecular species detected by sequencing have representative strains in culture (Apr 2017): http://www.tandfonline.com/doi/full/10.1080/19490976.2017.1320468
Using advanced metagenomics techniques, researchers have found that conventional culture-based lab tests may misdiagnose as many as half of the microbial causes of diarrheal diseases in children (Nov 2019) https://web.archive.org/web/20240706184501/https://news.gatech.edu/news/2019/11/18/metagenomics-unlocks-unknowns-diarrheal-disease-cases-children
2017: Stanford study using shotgun sequencing says we still don't know 99% of human microbes: https://archive.is/wgucb
2017: From an international database of more than 1,500 metagenomes, the UQ team reconstructed the individual genomes of 7,280 new bacteria and 623 new archaea. Of these microorganisms, roughly a third were unlike anything scientists had seen before, warranting the creation of 17 new bacterial phylums and three new achaeal phylums. https://futurism.com/scientists-just-discovered-organisms-that-are-distinct-from-any-life-forms-known-to-science/
2017: NIH Microbiome Project Triples Number of Previously Identified Bacterial Genes: https://www.genengnews.com/gen-news-highlights/nih-microbiome-project-triples-number-of-previously-identified-bacterial-genes/81255000
2018: Researchers have used artificial intelligence (AI) to discover nearly 6,000 previously unknown species of virus https://www.nature.com/articles/d41586-018-03358-3
2018: Sanguibacter massiliensis sp. nov., Actinomyces minihominis sp. nov., Clostridium minihomine sp. nov., Neobittarella massiliensis gen. nov., and Miniphocibacter massiliensis gen. nov., new bacterial species isolated by culturomics from human stool samples https://www.sciencedirect.com/science/article/pii/S2052297518300222
2018: Researchers have discovered more than 200 previously unknown viruses in a category whose members cause illnesses such as influenza and haemorrhagic fevers. https://www.nature.com/articles/d41586-018-04102-7
2018: About half of all oral bacteria are uncultivable https://www.frontiersin.org/articles/10.3389/fphys.2018.00342/full
2018: How reliable is diagnostic testing for Zika? Almost two thirds of all laboratories showed false-positive or false-negative results. https://www.eurekalert.org/pub_releases/2018-03/gcfi-hri030118.php
2019: Thousands Of New Microbiome Species Found Living on the Human Body. The researchers estimate one of the new species is the seventh most prevalent intestinal microbe in the human microbiome http://blogs.discovermagazine.com/d-brief/2019/01/17/population-human-microbiome-new-species-western
2019: More than 100 new gut bacteria discovered in human microbiome https://www.sciencedaily.com/releases/2019/02/190204114602.htm. A human gut bacterial genome and culture collection for improved metagenomic analyses https://www.nature.com/articles/s41587-018-0009-7
2019: Almost 2000 unknown bacteria discovered in the human gut https://www.ebi.ac.uk/about/news/press-releases/2000-unknown-gut-bacteria-discovered. A new genomic blueprint of the human gut microbiota https://www.nature.com/articles/s41586-019-0965-1
2019: "Given that bacterial functions are conserved across taxonomic groups, we propose that studying microbial functioning may be more productive than a purely taxonomic approach" https://www.frontiersin.org/articles/10.3389/fpsyt.2019.00034/full
2019: "Current gold standard sequencing procedures do not permit the determination of taxa abundances per gram of stool, but only provide proportional information on the fraction of the microbiota belonging to a particular genus in the sequenced library. Changes in total microbial density in faecal samples might be a key feature of a dysbiotic ecosystem and therefore a crucial element in microbiome-based diagnostics. Amplicon sequencing provides no information on metabolic potential, and library preparation biases exaggerate the relative abundance of dominant taxa" https://www.tandfonline.com/doi/full/10.1080/17843286.2019.1583782
2019: "It's not enough to study the composition, or the increase or decrease of a species. We also have to understand how the microbiota sense us, and how they change their 'behavior' accordingly." https://www.eurekalert.org/pub_releases/2019-05/asfm-hsb051019.php
2019: Research conducted by scientists from Harvard Medical School and Joslin Diabetes Center uncovered a "staggering microbial gene diversity". More than half of the bacterial genes examined occurred only once (called “singletons”) and were specific to each individual https://hms.harvard.edu/news/microbial-fingerprinting
2021: Scientists identify over 140,000 virus species in the human gut, more than half of which have never been seen before (Feb 2021) https://www.eurekalert.org/pub_releases/2021-02/wtsi-sio021721.php
2021: Thousands of previously unknown phages discovered in whole-community human gut metagenomes https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-021-01017-w
2021: We found more than 54,000 viruses in people’s poo — and 92% were previously unknown to science (Jun 2021) https://theconversation.com/we-found-more-than-54-000-viruses-in-peoples-poo-and-92-were-previously-unknown-to-science-163258 Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome.
2021: "We show substantial temporal variation for most major gut genera; we find that for 78% of microbial genera, day-to-day absolute abundance variation is substantially larger within than between individuals, with up to 100-fold shifts over the study period. Our results suggest that to increase diagnostic as well as target discovery power, studies could adopt a repeated measurement design and/or focus analysis on community-wide microbiome descriptors and indices" https://www.nature.com/articles/s41467-021-27098-7
2022: An expanded reference map of the human gut microbiome reveals hundreds of previously unknown species https://www.nature.com/articles/s41467-022-31502-1
2023: Scientists identify thousands of unknown viruses in babies’ diapers https://www.washingtonpost.com/health/2023/04/23/babies-gut-diaper-study/ Expanding known viral diversity in the healthy infant gut.
2024: Scientists discover 18 new species of gut microbes. Global diversity of enterococci and description of 18 previously unknown species https://phys.org/news/2024-02-scientists-species-gut-microbes-antibiotic.html
2024: Bacterial ‘flipping’ allows genes to encode multiple versions of themselves and assume different forms, altering a core understanding of genetics (Sep 2024) https://forum.humanmicrobiome.info/threads/bacterial-flipping-allows-genes-to-encode-multiple-versions-of-themsel.621/ Intragenic DNA inversions expand bacterial coding capacity.
Reproducibility and standards are a significant issue [1][2][3][4][5][6].
Time of sample collection is critical for the replicability of microbiome analyses (July 2024) https://forum.humanmicrobiome.info/threads/new-findings-may-fix-the-replicability-crisis-in-microbiome-research-j.461/ "As little as four hours after a mouse eats breakfast, nearly 80 percent of its microbiome is different"
Commercial testing:
Researchers call for regulation of direct-to-consumer microbiome tests. The DTC microbiome testing industry needs more regulation (Mar 2024) https://forum.humanmicrobiome.info/threads/researchers-call-for-regulation-of-direct-to-consumer-microbiome-tests.305/ "There is no scientifically agreed-upon definition of a 'healthy' microbiome; the microbiome is dynamic and changes frequently; there is no clinical proof that these products work; and no standardization in the processes involved. The recommended interventions have not been clinically validated or had their claims evaluated by the FDA. The tests could do harm by convincing a person to delay medical care."
Direct-to-consumer microbiome testing needs regulation (Jul 2024, editorial) https://forum.humanmicrobiome.info/threads/researchers-call-for-regulation-of-direct-to-consumer-microbiome-tests.305/post-1076 "substantial uncertainty exists in the field, raising concerns about the benefits and harms for consumers"
Lucy Mailing's comprehensive guide, comparing the various available tests: https://www.lucymailing.com/a-comprehensive-guide-to-stool-and-microbiome-testing/
Current (2024) commercial testing has very limited value. Here's a great write up by a microbiologist about it. More: [1][2][3][4] - including commentary from Rob Knight and others. A real life example. Another researcher/professor in the field agreeing. Excellent podcast that supports and gets into the details. And still in 2021.
A major factor is also that most testing is only for bacteria, but it's looking like phages might be more important. There's also fungi and archaea.
Comparison between 16S rRNA and shotgun sequencing (Jan 2021) https://www.nature.com/articles/s41598-021-82726-y
Most commercial tests are currently using 16s sequencing, which is mostly only accurate to the genus level. Data at this level is not especially useful [1][2][3][4][5][6]. But even when using shotgun sequencing, you get more details but the usefulness of those details is still limited and mostly not actionable.
Here are a few articles questioning the accuracy of these tests: [1][2][3]
Here are examples of the same stool sample sequenced by two different companies, showing different results. And even major differences for the same stool sample from the same company, done at the same time [1].
Nonsensical results like this are common. And these two studies [1][2] explain why. Essentially, many people's stools are not uniform, thus depending on which part of the stool you sample, you'll get different results. Thus homogenizing the stool prior to sampling will give more consistent results, but also changes the proportions of the results. This is likely a major problem with uBiome for instance, who use a swab method rather than whole stool.
Nov 2022: The GI Map Test is INACCURATE?! https://web.archive.org/web/20221108194110/https://old.reddit.com/r/HumanMicrobiome/comments/ypm08o/the_gi_map_test_is_inaccurate_nov_2022/ - video detailing major issues with the GI Map and other similar tests, such as GI360 by DDI, and GI Effects.
Performance of a new molecular assay for the detection of gastrointestinal pathogens (2020) https://www.microbiologyresearch.org/content/journal/acmi/10.1099/acmi.0.000160 "The purpose of this study was to evaluate the performance of a new molecular test (Diagnostics Solutions Laboratory GI-MAP) for the detection of bacterial and parasitic pathogens in stool samples spiked with known organisms. Highly variable results, poor level of specificity, many false positive results"
Various companies that do it: ubiome, genova, American Gut, viome, uBiota, doctor's data, bioscreen. Here's a comparison of the different microbes each test for.
Analysis of Viome: https://microbiomedigest.com/2019/04/25/a-review-of-the-recent-viome-preprint/
Here's an example report from ubiome's $90 explorer kit. And an example (and discussion) of their SmartGut kit that goes through a doctor.
Here's an example report from BioScreen, which goes through a doctor and seems a little more useful.
Example report from Genova's GI Effects.
Example report from Diagnostic Solutions GI Map: https://www.diagnosticsolutionslab.com/assets/documents/gi-map-sample-report.pdf - this one seems very useful.
Directlabs.com has a variety of tests: https://store.directlabs.com/ - https://directlabs.com/specialty-labs - The "Comprehensive Digestive Stool Analysis 2.0™ (CDSA 2.0)-Genova Kit" is probably the most useful one from them.
This is essentially the best input you can expect to get from sharing your results.
SIBO:
Small Intestinal Bacterial Overgrowth
Breath testing is unreliable, symptoms are non-specific, and the term itself is likely erroneous: https://humanmicrobiome.info/sibo/
FMT donor screening:
Screening stool donors for Fecal Microbiota Transplants (FMT).
H. Pylori: https://humanmicrobiome.info/h-pylori/
Blastocystis: https://humanmicrobiome.info/blastocystis
Cytomegalovirus in donors for fecal microbiota transplantation, the phantom menace? (Jun 2023, n=483) "Healthy volunteers with positive CMV serology do not shed CMV DNA in their stool, as detected by PCR or cell culture. This study provides another argument to remove CMV screening for FMT donors."
The pathogenicity of Entamoeba histolytica and Dientamoeba fragilis and their FMT transmission risk are subject to debate. In the United States, stool donors are no longer screened for Blastocystis hominis or Dientamoeba fragilis, and CHUV has adopted the same practice. https://smw.ch/index.php/smw/article/view/3472/5739#d119e205
Should the Faecal Microbiota Composition Be Determined to Certify a Faecal Donor? (Nov 2024) https://www.mdpi.com/2075-4418/14/23/2635 "clear criteria for microbial normality and health have yet to be established. Therefore, donor certification should focus more on clinical and lifestyle aspects"