In this commentary, we point to guidelines for performing human neuroimaging studies and their reporting in microbiota-gut-brain (MGB) articles. Moreover, we provide a view on interpretational issues in MGB studies, with a specific focus on gut microbiota–derived metabolites. Thus, extending the target article, we provide recommendations to the field to increase reproducibility and relevance of this type of MGB study.

We identify the significance and typical requirements of developmental analyses of the microbiome-gut-brain (MGB) in parents, offspring, and parent-offspring relations, which have particular importance for neurobehavioral outcomes in mammalian species, including humans. We call for a focus on behavioral measures of social-emotional function. Methodological approaches to interpreting relations between the microbiota and behavior are discussed.

Hooks et al. note that microbiota-gut-brain research suffers from serious methodological flaws and interpretative issues. We suggest two corrective measures: first, taking more seriously the need of interdisciplinary work; second, interpreting some of the methodological issues as ordinary challenges of standardization, typical of emerging disciplines.

Hooks et al. posit that gastrointestinal microbes alter the end state of development indirectly. Here, we present the immune system as the link that facilitates communication between the gut and the brain. Illustrating the case of autism spectrum disorder, we explicate the role of the immune system in responding to microbial dysbiosis by inducing an inflammatory state that affects neurodevelopment. We propose two models: directly, within the infant, and indirectly, via maternal and infant systems.

This comment expands on Hooks et al.’s criticism of the problematic and overly general uses of “stress” within the microbiota-gut-brain field. The comment concludes that, for the microbiota-gut-brain field (as for other fields drawing on “stress”), much work is yet to be done in terms of how we explore and understand biology vis-à-vis psychology.

The Hooks et al. review of microbiota-gut-brain (MGB) literature provides a constructive criticism of the general approaches encompassing MGB research. This commentary extends their review by: (a) highlighting capabilities of advanced systems-biology “-omics” techniques for microbiome research and (b) recommending that combining these high-resolution techniques with intervention-based experimental design may be the path forward for future MGB research.

The overblown, somewhat dramatic media interpretation of microbiota-gut-brain literature is highly misleading. This phenomenon is not new to neuroscience, wherein rapidly evolving research fields struggle to translate findings into clinical practice. Advances in microbiology might integrate our understanding of complex biological pathways that should be interpreted within neuropsychiatric symptom dimensions rather than specific disorders.

Some neurotropic enteroviruses hijack Trojan horse/raft commensal gut bacteria to render devastating biomimicking cryptic attacks on human/animal hosts. Such virus-microbe interactions manipulate hosts’ gut-brain axes with accompanying infection-cycle-optimizing central nervous system (CNS) disturbances, including severe neurodevelopmental, neuromotor, and neuropsychiatric conditions. Co-opted bacteria thus indirectly influence host health, development, behavior, and mind as possible “fair-weather-friend” symbionts, switching from commensal to context-dependent pathogen-like strategies benefiting gut-bacteria fitness.

Dietary fiber and prebiotics consistently modulate microbiota composition and function and hence may constitute a powerful tool in microbiota-gut-brain axis research. However, this is largely ignored in Hooks et al.’s analysis, which highlights the limitations of probiotics in establishing microbiome-mediated effects on neurobehavioral functioning and neglects discussing the potential of prebiotics in warranting the microbiota's role in such effects.

For gut microbiota to influence behavior, microorganisms should be able to interfere with specific brain neurochemical circuitries. Understanding these molecular mechanisms is a key task in the new microbiota-gut-brain field. Recent studies have revealed that one major mechanistic link is the modulation of neuropeptide signaling by homologous bacterial proteins acting both directly and indirectly via production of neuropeptide-reactive immunoglobulins.

Endorsing the view that commonsense conceptions are shaped by scientific claims provides an explanation for why microbiota-gut-brain (MGB) research might become incorporated into commonsense notions of health. But scientific claims also shape notions of personal identity, which accounts for why they can become entrenched in common sense even after they have been refuted by science.

The microbiota-gut-brain (MGB) field holds huge potential for understanding behavioral development and informing effective early interventions for psychological health. To realize this potential, factors that shape the MGB axis in infancy (i.e., breast milk) must be integrated into a systemic framework that considers salient behavioral outcomes. This is best accomplished applying network analyses in large prospective, longitudinal investigations in humans.

Here we argue that a multidisciplinary research approach, such as currently practised in the field of developmental cognitive neuroscience, is key to maintaining current momentum and to future-proof the field of microbiome-gut-brain research. Moreover, such a comprehensive approach will also bring us closer to our aims of translation and targeted intervention approaches to improve mental health and well-being.

We argue for the importance of looking at the microbiota-gut-brain axis from a human developmental perspective. For this purpose, we first briefly highlight emerging research with infants attesting that the microbiome plays a role in early brain and cognitive development. We then discuss the use of developmentally informed humanized mouse models and implications of microbiome research that go beyond probiotic administration.

The conclusions reached by Hooks et al. urge the field to investigate the complex multipathway interactions between the microbiome and the gut-brain axis to understand the potential causal relationships involved. Claims in the field of microbiota-gut-brain research remain problematic without appropriate controls and adequate statistical power. A crucial question that follows from the authors' extensive review is: “Why don't probiotics work?”

Much microbiota-gut-brain research focuses on the causal role of microbiomes as a whole, rather than their component parts: microbes. Hooks et al. find these whole-community explanations inadequate; however, they do not provide suggestions for better explanations. By appealing to proportionality – a criterion that can be used to develop more appropriate causal explanations – more accurate causal claims can be made.

Citation-based metrics are increasingly used as a proxy to define representative, considerable, or significant papers. We challenge this belief by taking into account factors that may play a role in providing citations to a manuscript and whether/how those highly cited studies could shape a scientific field. A different approach to summarisation of relevant core publications within a topic is proposed.

The microbiota-gut-brain (MGB) axis field is at an exciting stage, but the most recent developments in microbiota research still have to find their way into MGB studies. Here we outline the standards for microbiome data generation, the appropriate statistical techniques, and the covariates that should be included in MGB studies to optimize discovery and translation to clinical applications.

The target article suggests inter-individual variability is a weakness of microbiota-gut-brain (MGB) research, but we discuss why it is actually a strength. We comment on how accounting for individual differences can help researchers systematically understand the observed variance in microbiota composition, interpret null findings, and potentially improve the efficacy of therapeutic treatments in future clinical microbiome research.

Our analysis of microbiota-gut-brain (MGB) research took MGB to task for some of its methods, concepts, and interpretations. Commentators then raised numerous issues about the neuroscientific and microbiome aspects of MGB and how it can be understood as a field. We respond by addressing the dimensionality (scope and depth) and causal focus of MGB.