Special Issues are flexible collections of articles, that have a common topic. The articles may be published in various monthly issues.


The human microbiome is a diverse consortium of bacteria, archaea, fungi, protozoa, and viruses that inhabit many parts of the human body. These consortia have been implicated in a range of vital physiological processes including energy homeostasis, metabolism, gut epithelial health, immunologic activity and neurobehavioral development. This Special Issue contains articles describing microbiota of different regions, including the oral cavity, the gut and the vagina as well as their implications on cancer, immunity and the brain. Moreover, treatment options are discussed such as microbiome transplantation or probotic therapy. In addition, articles about special microbiota, including the human virome or the infant microbiome are also part of this Special Issue.
Issue cover
Cover: The image shows a mouse colon section depicting epithelial cell nuclei in blue (DAPI stain) as well as mucus in yellow (UEA-1, a lectin stain) and green (a MUC-2 antibody). Image by Carolina Tropini, University of British Columbia (Canada) and Justin Sonnenburg, Stanford University (USA); image modified by MIC. The cover is published under the Creative Commons Attribution (CC BY) license. Enlarge issue cover


Beyond cells – The virome in the human holobiont

Rodrigo García-López, Vicente Pérez-Brocal and Andrés Moya

2019 | 10.15698/mic2019.09.689 | Full text | PDF | Abstract

Viromics, or viral metagenomics, is a relatively new and burgeoning field of research that studies the complete collection of viruses forming part of the microbiota in any given niche. It has strong foundations rooted in over a century of discoveries in the field of virology and recent advances in molecular biology and sequencing technologies. Historically, most studies have deconstructed the concept of viruses into a simplified perception of viral agents as mere pathogens, which demerits the scope of large-scale viromic analyses. Viruses are, in fact, much more than regular parasites. They are by far the most dynamic and abundant entity and the greatest killers on the planet, as well as the most effective geo-transforming genetic engineers and resource recyclers, acting on all life strata in any habitat. Yet, most of this uncanny viral world remains vastly unexplored to date, greatly hindered by the bewildering complexity inherent to such studies and the methodological and conceptual limitations. Viromic studies are just starting to address some of these issues but they still lag behind microbial metagenomics. In recent years, however, higher-throughput analysis and resequencing have rekindled interest in a field that is just starting to show its true potential. In this review, we take a look at the scientific and technological developments that led to the advent of viral and bacterial metagenomics with a particular, but not exclusive, focus on human viromics from an ecological perspective. We also address some of the most relevant challenges that current viral studies face and ponder on the future directions of the field.

Forty-five-year evolution of probiotic therapy

Scarlett Puebla-Barragan and Gregor Reid

2019 | 10.15698/mic2019.04.673 | Full text | PDF | Abstract

In the past forty-five years, the field of probiotics has grown from a handful of laboratory studies and clinical ideas into a legitimate research and translational entity conferring multiple benefits to humans around the world. This has been founded upon three principles: (i) the need for alternatives to drugs that either have sub-optimal efficacy or severe adverse effects; (ii) a growing interest in natural products and microbes, in particular catalyzed by studies showing the extent of microbes within humans and on our planet; and (iii) evidence on the genetics and metabolic properties of probiotic strains, and clinical studies showing their effectiveness. While some manufacturers have sadly taken advantage of the market growth to sell supplements and foods they term probiotic, without the necessary human study evidence, there are more and more companies basing their formulations on science. Adherence to the definition of what constitutes a probiotic, conclusions based on tested products not generalizations of the whole field, and applications emanating from microbiome research identifying new strains that provide benefits, will make the next forty-five years significantly changed approaches to health management. Exciting applications will emerge for cardiovascular, urogenital, respiratory, brain, digestive and skin health, detoxification, as well as usage across the world’s ecosystems.

Gut microbial metabolites in depression: understanding the biochemical mechanisms

Giorgia Caspani, Sidney Kennedy, Jane A. Foster and Jonathan Swann

2019 | 10.15698/mic2019.10.693 | Full text | PDF | Abstract

Gastrointestinal and central function are intrinsically connected by the gut microbiota, an ecosystem that has co-evolved with the host to expand its biotransformational capabilities and interact with host physiological processes by means of its metabolic products. Abnormalities in this microbiota-gut-brain axis have emerged as a key component in the pathophysiology of depression, leading to more research attempting to understand the neuroactive potential of the products of gut microbial metabolism. This review explores the potential for the gut microbiota to contribute to depression and focuses on the role that microbially-derived molecules – neurotransmitters, short-chain fatty acids, indoles, bile acids, choline metabolites, lactate and vitamins – play in the context of emotional behavior. The future of gut-brain axis research lies is moving away from association, towards the mechanisms underlying the relationship between the gut bacteria and depressive behavior. We propose that direct and indirect mechanisms exist through which gut microbial metabolites affect depressive behavior: these include (i) direct stimulation of central receptors, (ii) peripheral stimulation of neural, endocrine, and immune mediators, and (iii) epigenetic regulation of histone acetylation and DNA methylation. Elucidating these mechanisms is essential to expand our understanding of the etiology of depression, and to develop new strategies to harness the beneficial psychotropic effects of these molecules. Overall, the review highlights the potential for dietary interventions to represent such novel therapeutic strategies for major depressive disorder.

Influence of delivery and feeding mode in oral fungi colonization – a systematic review

Maria Joao Azevedo, Maria de Lurdes Pereira, Ricardo Araujo, Carla Ramalho, Egija Zaura and Benedita Sampaio-Maia

2020 | 10.15698/mic2020.02.706 | Full text | PDF | Abstract

Postnatal acquisition of microorganisms from maternal and environmental sources contributes to the child microbiome development. Several studies showed that the mode of delivery and breastfeeding may have impact on the oral bacterial colonization, however, the influence on oral fungal colonization is still unknown. We performed a systematic literature review on mother to child oral fungi transmission, namely regarding the association between the mode of delivery and breastfeeding in oral yeast colonization. Our analysis revealed no significant differences between the oral mycobiome of breastfed and bottle-fed children. As for the delivery mode, the majority of studies found a relation between fungal colonization and vaginal delivery. Candida albicans was the most commonly isolated fungi species. Our analysis suggests that maternal breastfeeding does not seem to influence oral mycology, but vaginal delivery appears to promote oral yeast colonization in early life.

The influence of the microbiota on immune development, chronic inflammation, and cancer in the context of aging

Taylor N. Tibbs, Lacey R. Lopez and Janelle C. Arthur

2019 | 10.15698/mic2019.08.685 | Full text | PDF | Abstract

From birth, the microbiota plays an essential role in human development by educating host immune responses. Proper maturation of the immune system perturbs chronic inflammation and the pathogenesis of disease by preventing inappropriate immune responses. While many have detailed the roles of specific microbial groups in immune development and human disease, it remains to be elucidated how the microbiota influences the immune system during aging. Furthermore, it is not yet understood how age-related changes to the microbiota and immune system influence the development of age-related diseases. In this review, we outline the role of the microbiota in immune system development as well as functional changes that occur to immune cell populations during immunosenescence. In addition, we highlight how commensal microbes influence the pathogenesis of cancer, a prominent disease of aging. The information provided herein suggests that age-related changes to the microbiota and immune system should be considered in disease treatment and prevention strategies.

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