Fungal Research

Publication Analysis 1999-2010
by Kathleen Gransalke, Labtimes 05/2012



Europe... ... and the World Most Cited Authors... ... and Papers

Most Cited Authors - Pictures



Mycelium of Agrocybe praecox, a fungus studied for its pollutant-degrading abilities. (Photo: Grit Kabiersch, University of Helsinki)

A world without fungi would be totally boring, said Hauke Harms, Head of the Department of Environmental Microbiology at the Helmholtz Centre for Environmental Research in Leipzig, Germany, to Lab Times last year. Not only boring but maybe even unthinkable, we might add, considering the fact that fungi have many precious talents. They decompose organic matter, are vital symbiosis partners as well as the source of antibiotics and play leading roles in the production of staple foods like bread and, for some people more importantly, beer.

But there’s also a dark side to them. Fungi are responsible for many horrors in their sister kingdoms: A fungus by the name of Batrachochytrium dendrobatidis has come to worldwide fame as the “frog killer”, driving hundreds of amphibian species to the brink of extinction. And pictures of the “mind control fungus” Ophiocordyceps unilateralis, growing out of an ant’s thorax, have probably also etched into the minds of many. Not to mention all the crop plants succumbing to pathogenic fungi.

As limitless as their abilities are their numbers. Latest estimates speak of 5.1 million species encompassing yeasts, moulds, smuts and our beloved mushrooms, who have taken residence in a diverse range of partly rather unusual habitats. Recently, researchers from the University of Florence, for example, discovered that Saccharomyces cerevisiae ‘overwinters’ in the gut of queens of social wasps. However, from the five million species only a few have found their way into modern labs.

Out of the shadows?

What constitutes a “fungal researcher” was the main question we had to answer for this publication analysis. Does the fungus take centre stage in his or her research or does he or she use it only as a means to a cell biological end – to learn, for example, more about basic features of eukaryotes in general? What about the clinicians trying to understand and find treatment options for fungal infections? After a short debate, we decided to include all – phylogeneticists, medical mycologists as well as those interested in fungal genomics and cell biology. As long as fungi were involved one way or another, it counted.

This, however, led to the fact that “real mycologists” who are anyway not often granted a place under the research sun, are once again, condemned to a shadowy existence. Ironically, this fits perfectly to their study subjects.

After having agreed on the publication analysis participants, we again encountered the same methodological constraints that already impeded earlier analyses. As we previously stated, in order to compare performance of individual European countries in fungal research (as shown in the “blue” Table on p. 33), we had to restrict the study to explicit “fungi journals” selected from the category “Mycology” of Thomson Reuters’ database Web of Science, which we used for this analysis. Even though we are aware of the fact that many “top papers” are published in multidisciplinary journals like Nature, Science or PNAS, we had no choice but to omit these journals at least from this part of the analysis. The main reason for this omission is because Web of Science does not provide any reliable tools to automatically extract relevant fungal research articles from those multidisciplinary journals. Only the fungi expert journals were therefore consulted in the hope to avoid assigning too many “false positives” to individual countries.

We still believe, however, that such a “trimmed” survey provides sufficiently valid indicators for the countries’ overall productivity in fungal research. The rankings of the most-cited researchers and papers (see Tables on p. 34) were not subject to any analytical constraints. They could be analysed from publications in all journals.

The Netherlands oust England

Without any further explanations, let’s have a look at the individual countries’ performance in fungal research. Clear winner in this discipline is Germany; surprisingly followed by The Netherlands. England, who, in most rankings had a monopoly for the top two spots, this time only made it to third place.

The Netherlands most likely owe their excellent result to the scientific output of the CBS-KNAW Fungal Biodiversity Centre in Utrecht, which besides doing research on fungal taxonomy, evolution, biology and ecology “maintains a world-renowned collection of living filamentous fungi, yeasts and bacteria”. Only the centre’s director, Pedro W. Crous, however, managed to enter the most-cited authors’ ranking (7th place) but it shouldn’t go unmentioned that some of his colleagues, namely Teun Boekhout and G. Sybren de Hoog, missed the top 30 only by a few citations.

The Netherlands’ good result was not the only surprise. Portugal did very well (13th place) compared to previous rankings, while Israel must have their research foci anywhere but on fungal research – they didn’t make the top 20 this time. Regarding mean citation rates, Scotland again came off as one of the winners, followed by Ireland – who were short of a few total citations to be included in the top 20 – and The Netherlands.

A look to the left and right of our continent revealed overwhelming fungal research supremacy. European researchers have published more than twice as many articles on fungi than their US colleagues and ten times as many as their Japanese and Chinese peers. Their overall citation number dwarfs those of several other countries. Europe’s reign, however, does not span all parameters. When it comes to citations per article, European papers clearly lose against the USA, Canada and Australia.

Infections dominate

As wide as the fields of fungal activity are the topics our top 30 researchers study. Crudely, they can be divided into four categories: fungal pathogenesis and infections, physiology, phylogeny/taxonomy and industrial exploitation. Researchers interested in the two former categories are the most numerous, taking up 26 of the 30 available spots including the top two spots. Thus, champion and vice champion, David W. Denning and Olivier Lortholary, outpaced all other “contestants” with their publications on aspergillosis, a fungally inflicted condition affecting a patient’s lungs, and candidosis or thrush, courtesy of Candida albicans.

Other top 30 researchers are more interested in the inner workings of a fungal cell. Johan Thevelein (10th), for example, wants to understand how yeasts sense nutrients and how different nutrients influence cellular activities like stress and growth. Ida van der Klei (27th) and Marten Veenhuis (22nd) are after peroxisomes, eukaryotic organelles involved in, amongst others, the degradation of very long chain fatty acids. Fungi, especially Ascomycota or sac fungi, are a good model system to study these organelles because of their peroxisome-derived “Woronin bodies”.

That fungi are especially well-suited for biotechnological approaches has been known for some time. Bärbel Hahn-Häger­dal (9th) recognised this too. In her long career, she has worked on improving the fermenting abilities of industrial yeast strains. Optimising industrially-used fungal strains is also Christian Kubicek’s (26th) line of research. His lab pets, however, are representatives of the genus Trichoderma, soil fungi employed as biocontrol agents in plants.

Fungi can thus provide answers to very different scientific questions. And with the knowledge that thousands, if not millions of species are still out there waiting to be discovered and analysed, this field of research is surely good for a few more revealing insights about our world.




Method

Articles appearing between 1999 and 2010 in ‘fungi research journals’ as listed by SCImago and Thomson Reuters’ Web of Science. The citation numbers are accurate as of July 2012. A country’s figures are derived from articles, where at least one author working in the respective European nation is included in the authors’ list. Israel is included because it is a member of many European research organisations and programmes (EMBO, FP7 of the EU...).

Citations of articles published between 1999 and 2010 were recorded up until July 2012 using the Web of Science database from Thomson Reuters. The “most-cited papers” had correspondence addresses in Europe or Israel.





Europe...

Country Citations Articles Cit./Art.
1.Germany20.5581.98210,4
2.Netherlands15.13498315,4
3.England12.2951.02512,0
4.France11.8461.16810,1
5.Spain10.8581.3638,0
6.Italy6.3827578,4
7.Sweden6.14350412,2
8.Scotland5.27827719,1
9.Austria5.23649210,6
10.Denmark4.59832214,3
11.Switzerland4.22535511,9
12.Belgium3.4863918,9
13.Portugal2.94125311,6
14.Norway2.89826211,1
15.Finland1.99018111,0
16.Turkey1.9543266,0
17.Poland1.8252796,5
18.Wales1.7639917,8
19.Hungary1.62614711,1
20.Czech Rep.1.5612975,3



... and the World

Citations Articles Cit./Art.
Europe95.95310.2239,4
USA53.5304.08413,1
Canada10.3761.0889,5
Australia10.03374113,5
Japan9.17769413,2
China8.1921.1677,0
South Korea6.9379737,1



Most Cited Authors...

Citations Articles
1.David W. Denning, Univ. Manchester11.487146
2.Olivier Lortholary, Univ. René Decartes Paris8.081194
3.Stephen G. Oliver, Univ. Manchester6.592132
4.Jens Nielsen, Chalmers Univ. Technol. Gothenburg6.264200
5.Jean-Paul Latge, Inst. Pasteur Paris5.513110
6.J. J. (Sef) Heijnen, Delf Univ. Technol.5.418160
7.Pedro W. Crous, CBS-KNAW Fungal Biodiv. Ctr. Utrecht5.278255
8.Frank C. Odds (emer.), Univ. Aberdeen5.060104
9.Bärbel Hahn-Hägerdal (emer.), Lund Univ.4.937100
10.Johan M. Thevelein, Kathol. Univ. Leuven4.867114
11.Neil A. R. Gow, Univ. Aberdeen4.615110
12.Claude Gaillardin, AgroParisTech 4.44791
13.Frans M. Klis, Univ. Amsterdam4.04670
14.Paul E. Verweij, Univ. Hosp. Nijmegen4.001137
15.Alistair J. P. Brown, Univ. Aberdeen3.94088
16.Jack Pronk, Delft Univ. Technol.3.912108
17.Juan-Luis Rodriguez-Tudela, Complutense Univ. Madrid3.795137
18.Ulrich Güldener, Helmholtz Ctr. Munich3.70019
19.Manuel Cuenca-Estrella, Inst. Salud Carlos III, Madrid3.503133
20.Oliver A. Cornely, Univ. Cologne 3.397101
21.Peter W. Piper, Univ. Sheffield3.35458
22.Marten Veenhuis, Univ. Groningen 3.309124
23.Josep Guarro, Univ. Rovira i Virgili3.300255
24.Bernhard Hube, Hans Knöll Inst. Jena3.19680
25.Nick D. Read, Univ. Edinburgh3.02551
26.Christian P. Kubicek, Vienna Univ. Technol.2.978115
27.Ida J. van der Klei, Univ. Groningen2.97499
28.Paola Bonfante, Univ. Turin2.851114
29.Françoise Dromer, Inst. Pasteur Paris2.84189
30.Hans-Christian Korting, LMU Munich († 2012)2.836133



... and Papers

Citations
1.Herbrecht, R; Denning, DW; Patterson, TF; [...] Schlamm, HT; Troke, PF; de Pauw, B
Voriconazole versus amphotericin B for primary therapy of invasive aspergillosis.
NEW ENGLAND JOURNAL OF MEDICINE 347(6): 408-415 AUG 8 2002
1318
2.Latge, JP
Aspergillus fumigatus and aspergillosis.
CLINICAL MICROBIOLOGY REVIEWS 12(2): 310-50 APR 1999
875
3.Wood, V; Gwilliam, R; Rajandream, MA; […] Ussery, D; Barrell, BG; Nurse, P
The genome sequence of Schizosaccharomyces pombe.
NATURE 415(6874): 871-80 FEB 21 2002
746
4.Dujon, B; Sherman, D; Fischer, G; […] Weissenbach, J; Wincker, P; Souciet, JL
Genome evolution in yeasts.
NATURE 430(6995): 35-44 JUL 1 2004
606
5.Hohmann S
Osmotic stress signaling and osmoadaptation in yeasts.
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS 66(2): 300-72 JUN 2002
604




Last Changed: 27.09.2012




Information 4


Information 5