Are Classic Microbiology Journals Facing Extinction?
Exploring the transformation of microbiology publishing and the future of scientific communication
The world of scientific publishing is undergoing a dramatic transformation unlike any in its 350-year history. Since the first academic journals emerged in the 17th century, scientific communication has maintained a relatively stable format—until now. Today, microbiology research stands at a crossroads, with traditional journals facing unprecedented challenges from new publishing models, open science advocates, political pressures, and evolving research practices.
The very foundation of how scientists share discoveries is being questioned, reshaped, and reimagined. This article explores whether classic scientific journals—those venerable institutions that have long served as gatekeepers of knowledge—are condemned to extinction or destined for evolution in the face of these powerful forces.
As we examine the trends, pressures, and innovations shaping microbiology publications, we uncover a fascinating story of adaptation, resistance, and change that affects not just scientists but everyone who benefits from scientific progress.
For centuries, established scientific journals have served as the cornerstone of academic communication, providing a validated record of scientific progress. In microbiology, titles like Nature Microbiology, Journal of Bacteriology, Trends in Microbiology, and Cell Host & Microbe have represented scientific excellence and authority.
Meticulous filtering of knowledge through rigorous expert evaluation before dissemination
Journal imprimatur conferred prestige on authors and credibility on findings
These publications developed meticulous peer-review systems designed to filter knowledge through rigorous expert evaluation before dissemination. The imprimatur of these journals conferred prestige on authors and credibility on findings, creating an ecosystem where publication in "high-impact" journals became the primary metric for career advancement, funding acquisition, and academic recognition 1 .
The Impact Factor (IF), first introduced in the 1960s, became the quantitative holy grail of this system—a single number that supposedly captured a journal's importance and influence. This metric increasingly dictated where scientists would submit their best work and what institutions would consider when making hiring and promotion decisions.
The system created a self-reinforcing hierarchy where prestigious journals became increasingly selective, and publication in them became increasingly competitive. This "publish or perish" culture dominated academic microbiology, shaping research priorities, methodologies, and career trajectories for generations of scientists.
The traditional journal system has increasingly emphasized metric parameters as objective measures of scientific quality and impact. These include not just Impact Factors but also citation counts, h-indexes, and altmetrics. This metric-focused approach has created significant perverse incentives in scientific publishing:
The proliferation of mass authorship presents particularly interesting challenges for microbiology. As seen in the autophagy guidelines papers—which boasted hundreds then thousands of contributors—the question of what constitutes meaningful authorship becomes increasingly difficult to answer 1 . These trends raise important questions about whether traditional evaluation systems can adequately accommodate modern collaborative research paradigms.
Beyond internal scientific challenges, traditional journals face external threats that could fundamentally alter their role. Recent political developments have introduced unprecedented uncertainty into scientific publishing. In the United States, government officials have proposed publishing bans that would prohibit federally-funded scientists from publishing in leading medical journals including JAMA, NEJM, and The Lancet .
The rationale behind these proposed restrictions centers on accusations of corruption and pharmaceutical influence. As Secretary of Health and Human Services Robert F. Kennedy Jr. stated, unless existing medical journals "change radically," the National Institutes of Health may establish its own journals and publish papers in-house .
Such moves would represent a seismic shift in government engagement with scientific publishing, potentially undermining the entire traditional journal ecosystem.
Virologist Angie Rasmussen captures the concern of many scientists: "Journals and the scientific process and the evidence-based process is really antithetical to what the current administration seems to be doing. I do expect them to continue pushing back against journals. This is part of a larger effort to really undermine science in the US" .
A fascinating example of how scientific publishing is evolving can be found in the Guidelines for the use and interpretation of assays for monitoring autophagy. First published in 2008 and updated every four years, these guidelines represent a unique publishing phenomenon that illustrates both the promises and challenges of modern scientific communication 1 .
The autophagy guidelines began as a modest effort to standardize methods in a rapidly expanding field. Led by Dr. D.J. Klionsky, Editor-in-Chief of Autophagy, the project aimed to compile essential criteria for demonstrating autophagy in one accessible document. What made this initiative unusual was its collaborative scale—the first edition included a substantial number of authors, but subsequent editions witnessed exponential growth in contributors 1 .
Requiring standardization across subdisciplines
Responsible for drafting specific methodological guidance
Involving all contributors
To resolve disagreements
Into a unified document
The autophagy guidelines have been remarkably successful by traditional metrics. As shown in the table below, the number of citations has grown dramatically with each edition, demonstrating their utility to the scientific community 1 .
| Edition | Publication Year | Number of Pages | Number of Authors | Total Citations |
|---|---|---|---|---|
| First | 2008 | 14 | 50 | 1,850 |
| Second | 2012 | 32 | 1,000 | 4,200 |
| Third | 2016 | 150 | 2,000 | 7,500 |
| Fourth | 2021 | 220 | 2,000 | 1,500* |
*Citation count for most recent edition continues to grow 1
However, this success comes with philosophical and practical questions about authorship and credit. With thousands of listed authors all receiving equal citation credit, the guidelines challenge traditional notions of scholarly contribution. As one critic noted: "It seems rather strange that among this plethora of authors, there is no mention of Y. Ohsumi, a Nobel Prize winner for his research on autophagy" 1 .
The guidelines also raise questions about how such mega-collaborations should be evaluated in academic contexts. If all authors receive equal credit, does this fairly represent their contributions? How should hiring and promotion committees evaluate such publications compared to traditional research articles? These questions remain unresolved as collaborative research models continue to expand.
Modern microbiology relies on sophisticated tools and reagents that enable precise manipulation and measurement of microbial systems. The table below highlights essential research reagents and their functions in contemporary studies.
| Reagent/Material | Primary Function | Application Examples |
|---|---|---|
| CRISPR-Cas9 systems | Gene editing | Bacterial genome modification, gene function studies |
| Fluorescent proteins | Cellular labeling | Tracking microbial populations, protein localization |
| 16S rRNA sequencing primers | Taxonomic identification | Microbial community analysis, microbiome studies |
| Antibiotic resistance markers | Selection of modified organisms | Genetic engineering, plasmid maintenance |
| LC3/GABARAP antibodies | Autophagy detection | Monitoring autophagy processes in infected cells |
| Cryo-EM reagents | Sample preparation | High-resolution structural biology of microbial complexes |
Faced with these multiple challenges, traditional journals are not passively awaiting extinction but are actively evolving. Several adaptive strategies have emerged:
Expanding open access options to address demands for public access to publicly-funded research
Implementing rigorous transparency standards to address reproducibility concerns
Embracing diverse content formats beyond traditional research articles
Establishing partnerships with preprint servers for rapid dissemination
Based on current trends, the future of microbiology publishing will likely feature several key developments:
The classic "research paper" will continue to evolve into multiple output types, each with different validation pathways. Microbiologists will share data, code, reagents, and protocols through specialized channels that receive appropriate credit.
Peer review may increasingly separate from journal branding, with validation occurring through post-publication review, preprint commenting, and social media discussion. Journal imprimaturs may become less important than community evaluation.
Artificial intelligence tools will increasingly assist with literature discovery, experimental design, and even peer review. These technologies may help manage information overload while identifying connections across disparate studies.
The research community will develop more nuanced assessment systems that better capture the impact and quality of scientific contributions beyond citation counts and journal brands. These might include contributions to protocols, datasets, software, and public engagement.
| Aspect | Traditional Model | Emerging Models |
|---|---|---|
| Dissemination | After peer review | Preprints with post-publication review |
| Access | Subscription-based | Open access, preprints |
| Authorship | Individual research groups | Massive collaborations |
| Outputs | Research articles | Data, code, protocols, articles |
| Evaluation | Journal prestige, citations | Alternative metrics, community assessment |
The evidence suggests that classic microbiology journals are not necessarily condemned to extinction but rather to substantial transformation. The functions they serve—validation, certification, dissemination, and archiving—remain essential to scientific progress. However, how these functions are implemented, by whom, and in what format is changing rapidly.
The most successful journals will be those that adapt to the new realities of mass collaboration, open science, and political scrutiny while maintaining the core values of rigorous peer review and editorial excellence. They will likely become more modular, transparent, and integrated with other research outputs beyond narrative articles.
For microbiologists, these changes offer both challenges and opportunities. The pressure to publish in high-impact journals may gradually diminish, replaced by more nuanced evaluation systems that recognize diverse contributions to science. The field may become more inclusive and collaborative, with faster dissemination and more robust findings.
Ultimately, while the containers of scientific knowledge may change, the essential value of reliable, validated science remains constant. As the autophagy guidelines demonstrate 1 , new publishing models can emerge that serve scientific needs in ways previously unimaginable. The future of microbiology publishing will likely be more diverse, accessible, and innovative than its past—and that evolution serves science and society alike.
As Rasmussen reminds us, "The peer review process is not perfect, and it's not intended to set things scientifically in stone forever and ever. But it is a way of getting experts to actually vet scientific results before they are published so that you can have more confidence in them" . However this process evolves, maintaining that confidence will remain the ultimate goal of scientific publishing—regardless of what form it takes.