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China leads microbiology research in the Nature Index, with its institutions holding five of the top 10 spots in the latest ranking. Its overall Share in the topic (310) is almost 60 points ahead of the United States (251), in second place.
The Chinese Academy of Sciences (CAS) sits comfortably in first place with more than double the Share of the second-ranked institution, Germany’s Max Planck Institute, one of three European institutions in the top 10.
The ranking below reflects institutions’ Share and article Count for microbiology-related research in Nature Index journals according to the 'Current Index', which at the time of writing covered the period from 1 November 2024 to 31 October 2025.
Some of the following information on institutions also gives rankings for biological sciences, which were taken from the Nature Index 2025 Research Leaders tables (covering the 2024 calendar year).
Leading institutions in microbiology in the Nature Index
Institutions are ranked by article Share for the period 1 November 2024 to 31 October 2025. Each institution's article count (Count) is also listed.
| Rank | Institution | Country | Count | Share |
|---|---|---|---|---|
| 1 | Chinese Academy of Sciences | China | 122 | 37.69 |
| 2 | Max Planck Society | Germany | 44 | 15.54 |
| 3 | Harvard University | United States | 26 | 11.47 |
| 4 | Shandong University | China | 30 | 9.82 |
| 5 | University of Chinese Academy of Sciences | China | 51 | 9.7 |
| 6 | French National Centre for Scientific Research | France | 55 | 9.64 |
| 7 | Nanjing Agricultural University | China | 17 | 8.94 |
| 8 | Swiss Federal Institute of Technology Zurich | Switzerland | 20 | 8.22 |
| 9 | Tsinghua University | China | 25 | 8.08 |
| 10 | The University of Tokyo | Japan | 17 | 8.01 |
1. Chinese Academy of Sciences
Share: 37.69
CAS in Beijing is the top-ranked institution in microbiology research, but it trailed Harvard University’s biological-sciences output in the Nature Index in 2024.
The Chinese institution forms the top two collaborative partnerships in microbiology in the Index. Its bilateral collaboration score (BCS) with the University of Chinese Academy of Sciences (UCAS) in Beijing is 30.18, far exceeding other partnerships. CAS and the University of Science and Technology of China (USTC) in Hefei, the second most prolific partnership in microbiology, has a BCS of 8.35. In both cases, CAS accounts for more than 70% of the BCS score.
CAS authors most frequently published microbiology papers in the journal Water Research, with an article count of 29 and a Share of 8.30. One article authored by CAS and USTC researchers describes how contaminants in agricultural wastewater such as heavy metals might increase risk of antibiotic resistance — a major public health challenge.
2. Max Planck Society, Germany
Share: 15.54
The Max Planck Society, based in Munich, is another institution that ranked lower (third) than Harvard in biological sciences in 2024, but was ahead of the US university for microbiology from November 2024 to October 2025, by four Share points.
Germany is the third-ranked country in microbiology research, after China and the United States.
Nature Communications was the most common Nature Index publication venue for Max Planck Society authors in microbiology; the institution was involved in 44 papers in the subject during the time period, 12 of which were published in the journal. One paper, published in late 2024, describes several new species of bacteria that live inside single‑celled organisms called ciliates, and perform ‘mitochondria‑like’ duties, such as energy production.
3. Harvard University, United States
Share: 11.47
Harvard in Cambridge, Massachusetts, remains a powerhouse in biological sciences in the Nature Index — more than 200 Share points ahead of CAS in the 2025 Research Leaders tables — so it’s unsurprising that it’s ranked highly in microbiology. The institution is only slightly ahead of Shandong University in Jinan, however, with a difference of just 1.65 Share points.
Harvard’s article Count in microbiology included seven papers in the Proceedings of the National Academy of Sciences of the United States of America — the most of any journal for Harvard-authored papers.
4. Shandong University, China
Share: 9.82
Shandong University significantly outperforms its biological-sciences standing in the Nature Index — 83rd in 2024 — by placing fourth in microbiology. It was involved in 30 papers in the topic from November 2024 to October 2025 compared with Harvard’s 26.
Shandong’s partnership with Nanjing Normal University formed the third most prolific collaboration in microbiology, with a BCS of 6.96.
5. University of Chinese Academy of Sciences, China
Share: 9.7
The Beijing-based UCAS is less than a Share point away from Shandong University, in fourth place, but the French National Centre for Scientific Research (CNRS) is very close behind.
With CAS, UCAS forms the most prolific partnership in microbiology in the Nature Index — though CAS is responsible for a much larger portion of the collaborative output.
When ranking institutions by their microbiology Count, UCAS comes in third, with 51, after CAS (122) and CNRS (55). Water Research, Nature Communications and Environmental Science and Technology are the journals with the most UCAS-authored microbiology papers in the current index window.
6. French National Centre for Scientific Research, France
Share: 9.64
CNRS was second only to CAS for microbiology Count in the Nature Index from November 2024 to October 2025, being involved in 55 papers. Fifteen of those articles are in Nature Communications, including a 2025 paper that examines plasmids — small, circular pieces of DNA in bacteria that often contain genes for antibiotic resistance — and suggests ways to potentially weaken their effects.
Headquartered in Paris, CNRS is France’s largest public research organization and one of the world’s leading institutions in fundamental science. It ranked 12th in biological sciences in the 2025 Research Leaders tables, which suggests that microbiology is an area of strength for France within that subject area.
7. Nanjing Agricultural University, China
Share: 8.94
A major outlier in this group, the Nanjing Agricultural University didn’t even rank in the top 100 for biological sciences in Nature Index 2025 Research Leaders. But it is less than a Share point behind CNRS in microbiology and just 2.53 Share points behind Harvard.
The university has a Count of just 17 in the topic — lower than most other institutions in the top 10 — suggesting that its researchers made strong contributions to the papers they co-authored. One such paper, published in ACS Nano in 2025, looked at ways to control porcine reproductive and respiratory syndrome virus, which causes a highly contagious disease in pigs.
8. Swiss Federal Institute of Technology Zurich, Switzerland
Share: 8.22
Ranked 8th in microbiology and 35th in biological sciences in the Nature Index 2025 Research Leaders, the Swiss Federal Institute of Technology Zurich (ETH Zurich) is one of Europe’s strongest institutions in both areas of research.
A public university with more than 25,000 students, ETH Zurich offers a joint microbiology and immunology PhD programme with the University of Zurich, which includes topics such as environmental and medical microbiology, bacterial and viral pathogenesis, infection biology and virology and veterinary bacteriology.
9. Tsinghua University, China
Share: 8.08
Another Beijing-based institution in this top 10, Tsinghua University sits within the top 30 of biological sciences rankings in the Nature Index 2025 Research Leaders.
Its microbiology Count of 25 papers includes nine articles in Water Research, many of which were related to antimicrobial resistance — a major area of study in microbiology research.
One paper, published in 2024, looked at viruses in wastewater-treatment sludge from antibiotic manufacturing plants to see whether they carry antibiotic-resistance genes that could be transferred to bacteria that are also in the sludge. The researchers found that the viral genomes rarely contained resistance genes, and the few that did were not a match for those in nearby bacteria, which suggests that viruses play only a minor role in spreading antibiotic resistance in this system.
10. The University of Tokyo, Japan
Share: 8.01
Japan’s only entry in the microbiology top 10 is the University of Tokyo. In the biological sciences, Japan came in sixth place in the Nature Index 2025 Research Leaders, which is one place down from its overall rank of 5th.
One paper co-authored by University of Tokyo researchers and published in Science in 2025 looked at ways to date the evolutionary stages of the earliest living organisms, based on fossil evidence. Using a variety of methods, the authors established when major bacterial groups are likely to have evolved and how they adapted to oxygen. The paper concludes that most bacteria probably arose in low-oxygen environments and only evolved oxygen use after Earth’s atmosphere changed.
Note: The data in this article were based on the 12-month window of data in the 'Current Index' that was available at the time of writing. This window updates monthly and therefore future Share and Count values may differ. For more information on the Nature Index, see our FAQs.
