Culturing Human Gut Microbiomes in the Laboratory

2021 ◽  
Vol 75 (1) ◽  
Author(s):  
Simone Renwick ◽  
Caroline M. Ganobis ◽  
Riley A. Elder ◽  
Connor Gianetto-Hill ◽  
Gregory Higgins ◽  
...  
Keyword(s):  
Current Knowledge ◽  
Axenic Culture ◽  
Model Systems ◽  
Annual Review ◽  
Publication Date ◽  
Human Gut ◽  
Complex Interactions ◽  
Viral Particles ◽  
Eukaryotic Microbes

The human gut microbiota is a complex community of prokaryotic and eukaryotic microbes and viral particles that is increasingly associated with many aspects of host physiology and health. However, the classical microbiology approach of axenic culture cannot provide a complete picture of the complex interactions between microbes and their hosts in vivo. As such, recently there has been much interest in the culture of gut microbial ecosystems in the laboratory as a strategy to better understand their compositions and functions. In this review, we discuss the model platforms and methods available in the contemporary microbiology laboratory to study human gut microbiomes, as well as current knowledge surrounding the isolation of human gut microbes for the potential construction of defined communities for use in model systems. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Vascularized Microfluidics and Their Untapped Potential for Discovery in Diseases of the Microvasculature

2021 ◽  
Vol 23 (1) ◽  
Author(s):  
David R. Myers ◽  
Wilbur A. Lam
Keyword(s):  
Biomedical Engineering ◽  
Blood Cells ◽  
Online Publication ◽  
State Of The Art ◽  
Annual Review ◽  
Publication Date ◽  
New Era ◽  
Complex Interactions ◽  
Microvascular Diseases

Microengineering advances have enabled the development of perfusable, endothelialized models of the microvasculature that recapitulate the unique biological and biophysical conditions of the microcirculation in vivo. Indeed, at that size scale (<100 μm)—where blood no longer behaves as a simple continuum fluid; blood cells approximate the size of the vessels themselves; and complex interactions among blood cells, plasma molecules, and the endothelium constantly ensue—vascularized microfluidics are ideal tools to investigate these microvascular phenomena. Moreover, perfusable, endothelialized microfluidics offer unique opportunities for investigating microvascular diseases by enabling systematic dissection of both the blood and vascular components of the pathophysiology at hand. We review ( a) the state of the art in microvascular devices and ( b) the myriad of microvascular diseases and pressing challenges. The engineering community has unique opportunities to innovate with new microvascular devices and to partner with biomedical researchers to usher in a new era of understanding and discovery of microvascular diseases. Expected final online publication date for the Annual Review of Biomedical Engineering, Volume 23 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Origin and Early Evolution of the Eukaryotic Cell

2021 ◽  
Vol 75 (1) ◽  
Author(s):  
Toni Gabaldón
Keyword(s):  
Current Knowledge ◽  
Eukaryotic Cell ◽  
Early Evolution ◽  
Annual Review ◽  
Publication Date ◽  
Eukaryotic Evolution ◽  
Life Itself ◽  
Metabolic Interactions ◽  
Phylogenomic Analyses ◽  
Origin Of Eukaryotes

The origin of eukaryotes has been defined as the major evolutionary transition since the origin of life itself. Most hallmark traits of eukaryotes, such as their intricate intracellular organization, can be traced back to a putative common ancestor that predated the broad diversity of extant eukaryotes. However, little is known about the nature and relative order of events that occurred in the path from preexisting prokaryotes to this already sophisticated ancestor. The origin of mitochondria from the endosymbiosis of an alphaproteobacterium is one of the few robustly established events to which most hypotheses on the origin of eukaryotes are anchored, but the debate is still open regarding the time of this acquisition, the nature of the host, and the ecological and metabolic interactions between the symbiotic partners. After the acquisition of mitochondria, eukaryotes underwent a fast radiation into several major clades whose phylogenetic relationships have been largely elusive. Recent progress in the comparative analyses of a growing number of genomes is shedding light on the early events of eukaryotic evolution as well as on the root and branching patterns of the tree of eukaryotes. Here I discuss current knowledge and debates on the origin and early evolution of eukaryotes. I focus particularly on how phylogenomic analyses have challenged some of the early assumptions about eukaryotic evolution, including the widespread idea that mitochondrial symbiosis in an archaeal host was the earliest event in eukaryogenesis. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Modeling Food Particle Systems: A Review of Current Progress and Challenges

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Lennart Fries
Keyword(s):  
Particle Systems ◽  
Model Systems ◽  
Annual Review ◽  
Publication Date ◽  
Food Particle ◽  
Adequate Model ◽  
Food Powders ◽  
Contact Models ◽  
Physical Phenomena ◽  
The Impact

For many years, food engineers have attempted to describe physical phenomena such as heat and mass transfer in food via mathematical models. Still, the impact and benefits of computer-aided engineering are less established in food than in most other industries today. Complexity in the structure and composition of food matrices are largely responsible for this gap. During processing of food, its temperature, moisture, and structure can change continuously, along with its physical properties. We summarize the knowledge foundation, recent progress, and remaining limitations in modeling food particle systems in four relevant areas: flowability, size reduction, drying, and granulation and agglomeration. Our goal is to enable researchers in academia and industry dealing with food powders to identify approaches to address their challenges with adequate model systems or through structural and compositional simplifications. With advances in computer simulation capacity, detailed particle-scale models are now available for many applications. Here, we discuss aspects that require further attention, especially related to physics-based contact models for discrete-element models of food particle systems. Expected final online publication date for the Annual Review of Chemical and Biomolecular Engineering, Volume 12 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

In Vivo Dynamics of the Latent Reservoir for HIV-1: New Insights and Implications for Cure

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Janet D. Siliciano ◽  
Robert F. Siliciano
Keyword(s):  
Limit Of Detection ◽  
Latent Reservoir ◽  
Annual Review ◽  
Publication Date ◽  
Viral Rebound ◽  
Major Barrier ◽  
Persons Living With Hiv ◽  
Recent Developments ◽  
Hiv 1

Although antiretroviral therapy (ART) can reduce viremia to below the limit of detection and allow persons living with HIV-1 (PLWH) to lead relatively normal lives, viremia rebounds when treatment is interrupted. Rebound reflects viral persistence in a stable latent reservoir in resting CD4+ T cells. This reservoir is now recognized as the major barrier to cure and is the focus of intense international research efforts. Strategies to cure HIV-1 infection include interventions to eliminate this reservoir, to prevent viral rebound from the reservoir, or to enhance immune responses such that viral replication is effectively controlled. Here we consider recent developments in understanding the composition of the reservoir and how it can be measured in clinical studies. We also discuss exciting new insights into the in vivo dynamics of the reservoir and the reasons for its remarkable stability. Finally we discuss recent discoveries on the complex processes that govern viral rebound. Expected final online publication date for the Annual Review of Pathology: Mechanisms of Disease, Volume 17 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

A Comparative Overview of the Intracellular Guardians of Plants and Animals: NLRs in Innate Immunity and Beyond

2021 ◽  
Vol 72 (1) ◽  
Author(s):  
Zane Duxbury ◽  
Chih-hang Wu ◽  
Pingtao Ding
Keyword(s):  
Immune Responses ◽  
Genetic Architecture ◽  
Pathogen Detection ◽  
Current Knowledge ◽  
Plant Immunity ◽  
Innate Immune ◽  
Plant Biology ◽  
Annual Review ◽  
Publication Date ◽  
Nucleotide Binding Domain

Nucleotide-binding domain leucine-rich repeat receptors (NLRs) play important roles in the innate immune systems of both plants and animals. Recent breakthroughs in NLR biochemistry and biophysics have revolutionized our understanding of how NLR proteins function in plant immunity. In this review, we summarize the latest findings in plant NLR biology and draw direct comparisons to NLRs of animals. We discuss different mechanisms by which NLRs recognize their ligands in plants and animals. The discovery of plant NLR resistosomes that assemble in a comparable way to animal inflammasomes reinforces the striking similarities between the formation of plant and animal NLR complexes. Furthermore, we discuss the mechanisms by which plant NLRs mediate immune responses and draw comparisons to similar mechanisms identified in animals. Finally, we summarize the current knowledge of the complex genetic architecture formed by NLRs in plants and animals and the roles of NLRs beyond pathogen detection. Expected final online publication date for the Annual Review of Plant Biology, Volume 72 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Compositional, Structural, and Kinetic Aspects of Lipid Digestion and Bioavailability: In Vitro, In Vivo, and Modeling Approaches

2022 ◽  
Vol 13 (1) ◽  
Author(s):  
Sébastien Marze
Keyword(s):  
Annual Review ◽  
Publication Date ◽  
Lipid Digestion ◽  
Modeling Approaches ◽  
Digestion Kinetics ◽  
Food Design ◽  
Structural Aspects ◽  
Development And Evolution

Lipid digestion and bioavailability are usually investigated separately, using different approaches (in vitro, modeling, in vivo). However, a few inclusive studies show that their kinetics are closely linked. Lipid bioavailability kinetics is likely involved in the development and evolution of several diseases, so lipid digestion kinetics could be involved as well and can be modulated by food design or combination. To illustrate this possibility, the compositional and structural aspects of lipid digestion kinetics, as investigated using in vitro and modeling approaches, are presented first. Then, in vivo and mixed approaches enabling the study of both kinetics are reviewed and discussed. Finally, disparate modeling approaches are introduced, and a unifying modeling scheme is proposed, opening new perspectives for understanding the role and interactions of various factors (chemical, physical, and biological) involved in lipid metabolism. Expected final online publication date for the Annual Review of Food Science and Technology, Volume 13 is March 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Advances in Microbiome Research for Animal Health

2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Raquel S. Peixoto ◽  
Derek M. Harkins ◽  
Karen E. Nelson
Keyword(s):  
Current Knowledge ◽  
Animal Health ◽  
Biodiversity Loss ◽  
Emerging Diseases ◽  
Annual Review ◽  
Publication Date ◽  
Toxic Compounds ◽  
Symbiotic Interactions ◽  
Microbiome Research ◽  
And Behavior

Host-associated microbiomes contribute in many ways to the homeostasis of the metaorganism. The microbiome's contributions range from helping to provide nutrition and aiding growth, development, and behavior to protecting against pathogens and toxic compounds. Here we summarize the current knowledge of the diversity and importance of the microbiome to animals, using representative examples of wild and domesticated species. We demonstrate how the beneficial ecological roles of animal-associated microbiomes can be generally grouped into well-defined main categories and how microbe-based alternative treatments can be applied to mitigate problems for both economic and conservation purposes and to provide crucial knowledge about host–microbiota symbiotic interactions. We suggest a Customized Combination of Microbial-Based Therapies to promote animal health and contribute to the practice of sustainable husbandry. We also discuss the ecological connections and threats associated with animal biodiversity loss, microorganism extinction, and emerging diseases, such as the COVID-19 pandemic. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 9 is February 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Workplace Envy

2020 ◽  
Vol 8 (1) ◽  
Author(s):  
Michelle K. Duffy ◽  
KiYoung Lee ◽  
Elizabeth A. Adair
Keyword(s):  
Organizational Behavior ◽  
Online Publication ◽  
Current Knowledge ◽  
Cross Cultural ◽  
Future Research ◽  
Annual Review ◽  
Publication Date ◽  
The Past ◽  
Current Knowledge Base ◽  
Practical Implications

In the past 20 years, there has been a growing interest in the phenomenon of workplace envy. This article provides an overarching review and analysis of the workplace envy literature. We first consider conceptual and measurement challenges facing envy researchers. We then review the current knowledge base in the research with a focus on synthesizing what we have learned regarding workplace envy's transmutations, highlighting directions for future research. We explore two relatively understudied areas in the envy literature—antecedents of envy and the experience of being envied. We discuss methodologies used in the literature to study envy and outcomes and conclude with a focus on cross-cultural and practical implications. Expected final online publication date for the Annual Review of Organizational Psychology and Organizational Behavior, Volume 8 is January 21, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Critical Phenomena in Plasma Membrane Organization and Function

2020 ◽  
Vol 72 (1) ◽  
Author(s):  
Thomas R. Shaw ◽  
Subhadip Ghosh ◽  
Sarah L. Veatch
Keyword(s):  
Plasma Membrane ◽  
Critical Phenomena ◽  
Model Systems ◽  
Annual Review ◽  
Publication Date ◽  
Membrane Composition ◽  
Lipid Organization ◽  
And Function ◽  
Lateral Organization ◽  
Liquid Liquid Phase Separation

Lateral organization in the plane of the plasma membrane is an important driver of biological processes. The past dozen years have seen increasing experimental support for the notion that lipid organization plays an important role in modulating this heterogeneity. Various biophysical mechanisms rooted in the concept of liquid–liquid phase separation have been proposed to explain diverse experimental observations of heterogeneity in model and cell membranes with distinct but overlapping applicability. In this review, we focus on the evidence for and the consequences of the hypothesis that the plasma membrane is poised near an equilibrium miscibility critical point. Critical phenomena explain certain features of the heterogeneity observed in cells and model systems but also go beyond heterogeneity to predict other interesting phenomena, including responses to perturbations in membrane composition. Expected final online publication date for the Annual Review of Physical Chemistry, Volume 72 is April 20, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Physiologically Based Modeling of Food Digestion and Intestinal Microbiota: State of the Art and Future Challenges. An INFOGEST Review

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Steven Le Feunteun ◽  
Ahmed Al-Razaz ◽  
Matthijs Dekker ◽  
Erwin George ◽  
Beatrice Laroche ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
Historical Background ◽  
Annual Review ◽  
Publication Date ◽  
Physiologically Based ◽  
The Future ◽  
Future Challenges ◽  
Full Picture ◽  
Food Digestion

This review focuses on modeling methodologies of the gastrointestinal tract during digestion that have adopted a systems-view approach and, more particularly, on physiologically based compartmental models of food digestion and host–diet–microbiota interactions. This type of modeling appears very promising for integrating the complex stream of mechanisms that must be considered and retrieving a full picture of the digestion process from mouth to colon. We may expect these approaches to become more and more accurate in the future and to serve as a useful means of understanding the physicochemical processes occurring in the gastrointestinal tract, interpreting postprandial in vivo data, making relevant predictions, and designing healthier foods. This review intends to provide a scientific and historical background of this field of research, before discussing the future challenges and potential benefits of the establishment of such a model to study and predict food digestion and absorption in humans. Expected final online publication date for the Annual Review of Food Science and Technology, Volume 12 is March 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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