Better nanoscience through open, collaborative, and critical discussions.

We aim to foster a discussion of science correction and of how individual researchers can improve the quality and control of scientific production. This is crucial because although the maintenance of rigorous standards and the scrupulous control of research findings and methods are sometimes taken for granted, in practice, we are routinely confronted with articles that contain errors.

Epistemic misalignments in microbiome research.

We argue that microbiome research should be more reflective on the methods that it relies on to build its datasets due to the danger of facing a methodological problem which we call "epistemic misalignment." An epistemic misalignment occurs when the method used to answer specific scientific questions does not track justified answers, due to the material constraints imposed by the very method. For example, relying on 16S rRNA to answer questions about the function of the microbiome generates epistemic misalignments, due to the different temporal scales that 16S rRNA provides information about and the temporal scales that are required to know about the functionality of some microorganisms. We show how some of these exist in contemporary microbiome science and urge microbiome scientists to take some measures to avoid them, as they may question the credibility of the field as a whole.

Minding the gut: extending embodied cognition and perception to the gut complex.

Scientific and philosophical accounts of cognition and perception have traditionally focused on the brain and external sense organs. The extended view of embodied cognition suggests including other parts of the body in these processes. However, one organ has often been overlooked: the gut. Frequently conceptualized as merely a tube for digesting food, there is much more to the gut than meets the eye. Having its own enteric nervous system, sometimes referred to as the "second brain," the gut is also an immune organ and has a large surface area interacting with gut microbiota. The gut has been shown to play an important role in many physiological processes, and may arguably do so as well in perception and cognition. We argue that proposals of embodied perception and cognition should take into account the role of the "gut complex," which considers the enteric nervous, endocrine, immune, and microbiota systems as well as gut tissue and mucosal structures. The gut complex is an interface between bodily tissues and the "internalized external environment" of the gut lumen, involved in many aspects of organismic activity beyond food intake. We thus extend current embodiment theories and suggest a more inclusive account of how to "mind the gut" in studying cognitive processes.

Multidisciplinary of anti-COVID-19 battle: from immunological weapons to ecological interventions.

The COVID-19 pandemic is not just a medical and epidemiological problem. In fact, its impact concerns numerous aspects of human life (such as social and the political-economic dimension). This review aims at highlighting some crucial and neglected aspects of the pandemic in order to include them into a more general framework for the understanding of the phenomenon. Accordingly, it is structured as follows. First, after e brief recap of COVID-19 onset, it is argued the so-called proximate causes of the pandemic, i.e., the mechanisms by which viruses infect their hosts and the patterns of spread of the resulting pathologies, are not enough for a more adequate understanding of it. Second, it is shown how possible solutions to the risk of an upcoming pandemic involve studying the ultimate causes of this phenomenon. This means understanding not only how COVID-19 has become a global issue but also why it was possible for this to happen. Next, it is argued that is urgent to go to the root of the possible conditions: thus looking at the ecological dimension of diseases, the role of microorganisms in evolution, up to rethinking the organization of health systems. Third, to keep these very different perspectives together entails the study of COVID-19 from the point of view of the relationships between biological entities in a purely systemic dimension. Fourth, special attention is given to the symbiotic perspective offered by the study of the microbiota. It is argued how this perspective on microbiota provides an innovative interpretative lens with which to analyze various aspects (from the immunological to the ecosystemic one) of the pandemic. In conclusion, it is claimed that this field of study could perhaps offer not only elements that will be useful to make the treatment and containment strategies of the pandemic effective in its mechanisms, but also may suggest innovative elements for the solutions about the deep reasons that have made COVID-19 a global issue.

"Microbiota, symbiosis and individuality summer school" meeting report.

How does microbiota research impact our understanding of biological individuality? We summarize the interdisciplinary summer school on "Microbiota, symbiosis and individuality: conceptual and philosophical issues" (July 2019), which was supported by a European Research Council starting grant project "Immunity, DEvelopment, and the Microbiota" (IDEM). The summer school centered around interdisciplinary group work on four facets of microbiota research: holobionts, individuality, causation, and human health. The conceptual discussion of cutting-edge empirical research provided new insights into microbiota and highlights the value of incorporating into meetings experts from other disciplines, such as philosophy and history of science. Video Abstract.

Not just 'immunity': how the microbiota can reshape our approach to cancer immunotherapy.

Cancer immunotherapy refers to a set of approaches aiming at enhancing the immune system to fight cancer growth and spread. This variety of therapeutic approaches, especially those inhibiting immune checkpoints, have shown very promising results. Nevertheless, patients may respond differently to treatments and the efficacy of immunotherapy seems to be dependent on several factors that go beyond the molecular targeting of immune cells modulation. Here, we review how the activity of gut microbiota appears to be crucial in determining the effectiveness of some immunotherapeutic treatments, fostering or impeding the conditions under which treatments can work or not. Moreover, we discuss how these findings suggest not only extending the range of immunotherapeutic approaches but also reshaping our understanding of immunotherapy itself.

The link "Cancer and autoimmune diseases" in the light of microbiota: Evidence of a potential culprit.

Evidence establishes that chronic inflammation and autoimmunity are associated with cancer development and patients with a primary malignancy may develop autoimmune-like diseases. Despite immune dysregulation is a common feature of both cancer and autoimmune diseases, precise mechanisms underlying this susceptibility are not clarified and different hypotheses have been proposed, starting from genetic and environmental common features, to intrinsic properties of immune system. Moreover, as the development and use of immunomodulatory therapies for cancer and autoimmune diseases are increasing, the elucidation of this relationship must be investigated in order to offer the best and most secure therapeutic options. The microbiota could represent a potential link between autoimmune diseases and cancer. The immunomodulation role of microbiota is widely recognized and under eubiosis, it orchestrates both the innate and adaptive response of immunity, in order to discriminate and modulate the immune response itself in the most appropriate way. Therefore, a dysbiotic status can alter the immune tonus rendering the host prone to exogenous or endogenous infections, breaking the tolerance against self-components and activating the immune responses in an excessive (i.e. chronic inflammation) or deficient way, favoring the onset of neoplastic and autoimmune diseases.

Healthy axis: Towards an integrated view of the gut-brain health.

Despite the lack of precise mechanisms of action, a growing number of studies suggests that gut microbiota is involved in a great number of physiological functions of the human organism. In fact, the composition and the relations of intestinal microbial populations play a role, either directly or indirectly, to both the onset and development of various pathologies. In particular, the gastrointestinal tract and nervous system are closely connected by the so-called gut-brain axis, a complex bidirectional system in which the central and enteric nervous system interact with each other, also engaging endocrine, immune and neuronal circuits. This allows us to put forward new working hypotheses on the origin of some multifactorial diseases: from eating to neuropsychiatric disorders (such as autism spectrum disorders and depression) up to diabetes and tumors (such as colorectal cancer). This scenario reinforces the idea that the microbiota and its composition represent a factor, which is no longer negligible, not only in preserving what we call "health" but also in defining and thus determining it. Therefore, we propose to consider the gut-brain axis as the focus of new scientific and clinical investigation as long as the locus of possible systemic therapeutic interventions.

The Gut⁻Brain Axis in the Neuropsychological Disease Model of Obesity: A Classical Movie Revised by the Emerging Director "Microbiome".

The worldwide epidemic of obesity has become an important public health issue, with serious psychological and social consequences. Obesity is a multifactorial disorder in which various elements (genetic, host, and environment), play a definite role, even if none of them satisfactorily explains its etiology. A number of neurological comorbidities, such as anxiety and depression, charges the global obesity burden, and evidence suggests the hypothesis that the brain could be the seat of the initial malfunction leading to obesity. The gut microbiome plays an important role in energy homeostasis regulating energy harvesting, fat deposition, as well as feeding behavior and appetite. Dietary patterns, like the Western diet, are known to be a major cause of the obesity epidemic, probably promoting a dysbiotic drift in the gut microbiota. Moreover, the existence of a "gut⁻brain axis" suggests a role for microbiome on hosts' behavior according to different modalities, including interaction through the nervous system, and mutual crosstalk with the immune and the endocrine systems. In the perspective of obesity as a real neuropsychological disease and in light of the discussed considerations, this review focuses on the microbiome role as an emerging director in the development of obesity.

I've Gut A Feeling: Microbiota Impacting the Conceptual and Experimental Perspectives of Personalized Medicine.

In recent years, the human microbiota has gained increasing relevance both in research and clinical fields. Increasing studies seem to suggest the centrality of the microbiota and its composition both in the development and maintenance of what we call "health" and in generating and/or favoring (those cases in which the microbiota's complex relational architecture is dysregulated) the onset of pathological conditions. The complex relationships between the microbiota and human beings, which invest core notions of biomedicine such as "health" and "individual," do concern not only problems of an empirical nature but seem to require the need to adopt new concepts and new perspectives in order to be properly analysed and utilized, especially for their therapeutic implementation. In this contribution we report and discuss some of the theoretical proposals and innovations (from the ecological component to the notion of polygenomic organism) aimed at producing this change of perspective. In conclusion, we summarily analyze what impact and what new challenges these new approaches might have on personalized/person centred/precision medicine.