scholarly journals The soil in our microbial DNA informs about environmental interfaces across host and subsistence modalities

2020 ◽  
Vol 375 (1812) ◽  
pp. 20190577 ◽  
Author(s):  
Stephanie L. Schnorr
Keyword(s):  
Human Microbiome ◽  
Soil Microbial ◽  
Global Soil ◽  
Host Habitat ◽  
Microbiome Research ◽  
Health And Disease ◽  
Modern Context ◽  
Microbial Dna ◽  
Environmental Interfaces ◽  
Lifestyle Patterns

In this study, I use microbiome datasets from global soil samples and diverse hosts to learn whether soil microbial taxa are found in host microbiomes, and whether these observations fit the narrative that environmental interaction influences human microbiomes. A major motivation for conducting host-associated microbiome research is to contribute towards understanding how the environment may influence host physiology. The microbial molecular network is considered a key vector by which environmental traits may be transmitted to the host. Research on human evolution seeks evidence that can inform about the living experiences of human ancestors. This objective is substantially enhanced by recent work on ancient biomolecules from preserved microbial tissues, such as dental calculus, faecal sediments and whole coprolites. A challenge yet is to distinguish authentic biomolecules from environmental contaminants deposited contemporaneously, primarily from soil. However, we do not have sound expectations about the soil microbial elements arriving to host-associated microbiomes in a modern context. One assumption in human microbiome research is that proximity to the natural environment should affect biodiversity or impart genetic elements. I present evidence supporting the assumption that environmental soil taxa are found among host-associated gut taxa, which can recapitulate the surrounding host habitat ecotype. Soil taxa found in gut microbiomes relate to a set of universal ‘core’ taxa for all soil ecotypes, demonstrating that widespread host organisms may experience a consistent pattern of external environmental cues, perhaps critical for development. Observed differentiation of soil feature diversity, abundance and composition among human communities, great apes and invertebrate hosts also indicates that lifestyle patterns are inferable from an environmental signal that is retrievable from gut microbiome amplicon data. This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.

scholarly journals The microbiome in rheumatology: Where are we and where should we go?

2020 ◽  
pp. annrheumdis-2019-216631 ◽  
Author(s):  
Julia Manasson ◽  
Rebecca B Blank ◽  
Jose U Scher
Keyword(s):  
Clinical Practice ◽  
Human Health ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Future Directions ◽  
Sequencing Technologies ◽  
Challenges And Opportunities ◽  
Microbiome Research ◽  
Health And Disease ◽  
Micro Organisms

From birth, humans coexist and coevolve with trillions of micro-organisms inhabiting most body surfaces and cavities, referred to as the human microbiome. Advances in sequencing technologies and computational methods have propelled the exploration of the microbiome’s contribution to human health and disease, spearheaded by massive efforts such as the Human Microbiome Project and the Europe-based MetaHit Consortium. Yet, despite the accumulated body of literature and a growing awareness among patients, microbiome research in rheumatology has not had a key impact on clinical practice. Herein, we describe some of the landmark microbiome studies in autoimmunity and rheumatology, the challenges and opportunities of microbiome research and how to navigate them, advances in related fields that have overcome these pitfalls, and future directions of harnessing the microbiome for diagnostic and therapeutic purposes.

scholarly journals Integrating Microbiome Network: Establishing Linkages Between Plants, Microbes and Human Health

2019 ◽  
Vol 13 (1) ◽  
pp. 330-342 ◽  
Author(s):  
Suresh B. N. Krishna ◽  
Anamika Dubey ◽  
Muneer A. Malla ◽  
Richa Kothari ◽  
Chandrama P. Upadhyay ◽  
...  
Keyword(s):  
Human Health ◽  
Human Microbiome ◽  
Ecological Communities ◽  
Form Complex ◽  
The Past ◽  
Sequencing Technologies ◽  
Microbiome Research ◽  
Health And Disease ◽  
Metabolic Activities

The trillions of microbes that colonize and live around us govern the health of both plants and animals through a cascade of direct and indirect mechanisms. Understanding of this enormous and largely untapped microbial diversity has been the focus of microbial research from the past few decades or so. Amidst the advancements in sequencing technologies, significant progress has been made to taxonomically and functionally catalogue these microbes and also to establish their exact role in the health and disease state. In comparison to the human microbiome, plants are also surrounded by a vast diversity of microbes that form complex ecological communities that affect plant growth and health through collective metabolic activities and interactions. This plant microbiome has a substantial influence on human health and environment via its passage through the nasal route and digestive tract and is responsible for changing our gut microbiome. This review primarily focused on the advances and challenges in microbiome research at the interface of plant and human, and role of microbiome at different compartments of the body’s ecosystems along with their correlation to health and diseases. This review also highlighted the potential therapies in modulating the gut microbiota and technologies for studying the microbiome.

Inter-individual variation shapes the human microbiome

2019 ◽  
Vol 42 ◽  
Author(s):  
Emily F. Wissel ◽  
Leigh K. Smith
Keyword(s):  
Individual Differences ◽  
Individual Variation ◽  
Human Microbiome ◽  
Individual Variability ◽  
Microbiota Composition ◽  
Target Article ◽  
Microbiome Research

Abstract 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.

scholarly journals BOARD INVITED REVIEW: The pig microbiota and the potential for harnessing the power of the microbiome to improve growth and health1

2019 ◽  
Vol 97 (9) ◽  
pp. 3741-3757 ◽  
Author(s):  
Nirosh D Aluthge ◽  
Dana M Van Sambeek ◽  
Erin E Carney-Hinkle ◽  
Yanshuo S Li ◽  
Samodha C Fernando ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
Gut Microbiota ◽  
Therapeutic Potential ◽  
Animal Health ◽  
Microbial Colonization ◽  
Critical Importance ◽  
Specific Host ◽  
Microbiome Research ◽  
Health And Disease ◽  
The Impact

Abstract A variety of microorganisms inhabit the gastrointestinal tract of animals including bacteria, archaea, fungi, protozoa, and viruses. Pioneers in gut microbiology have stressed the critical importance of diet:microbe interactions and how these interactions may contribute to health status. As scientists have overcome the limitations of culture-based microbiology, the importance of these interactions has become more clear even to the extent that the gut microbiota has emerged as an important immunologic and metabolic organ. Recent advances in metagenomics and metabolomics have helped scientists to demonstrate that interactions among the diet, the gut microbiota, and the host to have profound effects on animal health and disease. However, although scientists have now accumulated a great deal of data with respect to what organisms comprise the gastrointestinal landscape, there is a need to look more closely at causative effects of the microbiome. The objective of this review is intended to provide: 1) a review of what is currently known with respect to the dynamics of microbial colonization of the porcine gastrointestinal tract; 2) a review of the impact of nutrient:microbe effects on growth and health; 3) examples of the therapeutic potential of prebiotics, probiotics, and synbiotics; and 4) a discussion about what the future holds with respect to microbiome research opportunities and challenges. Taken together, by considering what is currently known in the four aforementioned areas, our overarching goal is to set the stage for narrowing the path towards discovering how the porcine gut microbiota (individually and collectively) may affect specific host phenotypes.

scholarly journals Gut Microbiota and Host Metabolism: From Proof of Concept to Therapeutic Intervention

2021 ◽  
Vol 9 (6) ◽  
pp. 1302
Author(s):  
Patrice D. Cani ◽  
Emilie Moens de Hase ◽  
Matthias Van Hul
Keyword(s):  
Gut Microbiota ◽  
Research Field ◽  
Proof Of Concept ◽  
Clinical Implementation ◽  
Science Area ◽  
Microbiome Research ◽  
Fast Pace ◽  
Health And Disease ◽  
Underlying Mechanisms ◽  
Host Metabolism

The field of the gut microbiota is still a relatively young science area, yet many studies have already highlighted the translational potential of microbiome research in the context of human health and disease. However, like in many new fields, discoveries are occurring at a fast pace and have provided new hope for the development of novel clinical applications in many different medical conditions, not in the least in metabolic disorders. This rapid progress has left the field vulnerable to premature claims, misconceptions and criticism, both from within and outside the sector. Tackling these issues requires a broad collaborative effort within the research field and is only possible by acknowledging the difficulties and challenges that are faced and that are currently hindering clinical implementation. These issues include: the primarily descriptive nature of evidence, methodological concerns, disagreements in analysis techniques, lack of causality, and a rather limited molecular-based understanding of underlying mechanisms. In this review, we discuss various studies and models that helped identifying the microbiota as an attractive tool or target for developing various translational applications. We also discuss some of the limitations and try to clarify some common misconceptions that are still prevalent in the field.

scholarly journals Impact of the Human Microbiome in Forensic Sciences: a Systematic Review

2020 ◽  
Vol 86 (22) ◽  
Author(s):  
Manuel G. García ◽  
María D. Pérez-Cárceles ◽  
Eduardo Osuna ◽  
Isabel Legaz
Keyword(s):  
Systematic Review ◽  
Forensic Science ◽  
Human Microbiome ◽  
Geographical Location ◽  
Postmortem Interval ◽  
Forensic Sciences ◽  
Content Type ◽  
Microbiome Analysis ◽  
Location Of Death ◽  
Microbiome Research

ABSTRACT Numerous studies relate differences in microbial communities to human health and disease; however, little is known about microbial changes that occur postmortem or the possible applications of microbiome analysis in the field of forensic science. The aim of this review was to study the microbiome and its applications in forensic sciences and to determine the main lines of investigation that are emerging, as well as its possible contributions to the forensic field. A systematic review of the human microbiome in relation to forensic science was carried out by following PRISMA guidelines. This study sheds light on the role of microbiome research in the postmortem interval during the process of decomposition, identifying death caused by drowning or sudden death, locating the geographical location of death, establishing a connection between the human microbiome and personal items, sexual contact, and the identification of individuals. Actinomycetaceae, Bacteroidaceae, Alcaligenaceae, and Bacilli play an important role in determining the postmortem interval. Aeromonas can be used to determine the cause of death, and Corynebacterium or Helicobacter pylori can be used to ascertain personal identity or geographical location. Several studies point to a promising future for microbiome analysis in the different fields of forensic science, opening up an important new area of research.

Gut Feeling

2016 ◽  
Vol 33 (S1) ◽  
pp. S504-S505
Author(s):  
C. Cotta ◽  
G. Jesus ◽  
V. Vila Nova ◽  
C. Moreira
Keyword(s):  
Mental Disorders ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Bacterial Infections ◽  
Human Microbiome ◽  
Dietary Interventions ◽  
Scientific Databases ◽  
Antibiotic Drugs ◽  
Microbiome Research ◽  
Competing Interest

IntroductionThere is growing evidence of the importance of nutrition in mental disorders. Gut microbiota, influenced by environmental factors such as diet and stress, has been proposed as one of the players on a dynamic called gut-brain axis, which is thought to have an influence on behaviour and mental health.Objectives and aimsTo summarize recent evidence on the topic, and its potential role in psychiatric interventions.MethodsThe authors review updated literature collected from online scientific databases.ResultsThe development of the brain itself has been shown to be influenced by the gut microbiome. Research demonstrates that the composition of the microbiota has influence on behaviour through neuroendocrine and other neuroactive messengers production by the bacteria within the gut lumen. Studies in germ-free animals, animals exposed to bacterial infections, probiotic suplements or antibiotic drugs suggest a role for the gut microbiota in the regulation of anxiety, mood, cognition and pain. The gut microbiome has been implicated in brain disorders including anxiety and depression, multiple sclerosis, Alzheimer's disease, Parkinson's disease, and autism.ConclusionsThe treatment of mental disorders is usually based on pharmacological and psychotherapeutic interventions, and little attention is given to dietary interventions. The emerging field of research focused on the human microbiome suggests an important role for the gut microbiota in influencing brain development, behaviour and mood in humans, and points new strategies for developing novel therapeutics for mental disorders.Disclosure of interestThe authors have not supplied their declaration of competing interest.

Global soil microbial biomass decreases with aridity and land‐use intensification

2021 ◽  
Vol 30 (5) ◽  
pp. 1056-1069
Author(s):  
Xiaohua Wan ◽  
Xinli Chen ◽  
Zhiqun Huang ◽  
Han Y. H. Chen
Keyword(s):  
Land Use ◽  
Microbial Biomass ◽  
Soil Microbial Biomass ◽  
Soil Microbial ◽  
Land Use Intensification ◽  
Global Soil

Ethical, Legal, and Social Dimensions of Human Microbiome Research

2015 ◽  
pp. 163-171 ◽  
Author(s):  
Laura S. Achenbaum ◽  
Kieran C. O’Doherty ◽  
Amy L. McGuire
Keyword(s):  
Human Microbiome ◽  
Social Dimensions ◽  
Microbiome Research
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