scholarly journals Computational Modeling of the Human Microbiome

2020 ◽  
Vol 8 (2) ◽  
pp. 197
Author(s):  
Shomeek Chowdhury ◽  
Stephen S. Fong
Keyword(s):  
Computational Modeling ◽  
Human Health ◽  
Large Scale ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Microbial Composition ◽  
Site Specific ◽  
Microbiome Research ◽  
High Level ◽  
The Impact

The impact of microorganisms on human health has long been acknowledged and studied, but recent advances in research methodologies have enabled a new systems-level perspective on the collections of microorganisms associated with humans, the human microbiome. Large-scale collaborative efforts such as the NIH Human Microbiome Project have sought to kick-start research on the human microbiome by providing foundational information on microbial composition based upon specific sites across the human body. Here, we focus on the four main anatomical sites of the human microbiome: gut, oral, skin, and vaginal, and provide information on site-specific background, experimental data, and computational modeling. Each of the site-specific microbiomes has unique organisms and phenomena associated with them; there are also high-level commonalities. By providing an overview of different human microbiome sites, we hope to provide a perspective where detailed, site-specific research is needed to understand causal phenomena that impact human health, but there is equally a need for more generalized methodology improvements that would benefit all human microbiome research.

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 A CloudSat–CALIPSO View of Cloud and Precipitation Properties across Cold Fronts over the Global Oceans

2015 ◽  
Vol 28 (17) ◽  
pp. 6743-6762 ◽  
Author(s):  
Catherine M. Naud ◽  
Derek J. Posselt ◽  
Susan C. van den Heever
Keyword(s):  
Large Scale ◽  
Cold Front ◽  
Conveyor Belt ◽  
Low Level ◽  
Scale Parameters ◽  
Convective Clouds ◽  
Cold Fronts ◽  
Surface Front ◽  
High Level ◽  
The Impact

Abstract The distribution of cloud and precipitation properties across oceanic extratropical cyclone cold fronts is examined using four years of combined CloudSat radar and CALIPSO lidar retrievals. The global annual mean cloud and precipitation distributions show that low-level clouds are ubiquitous in the postfrontal zone while higher-level cloud frequency and precipitation peak in the warm sector along the surface front. Increases in temperature and moisture within the cold front region are associated with larger high-level but lower mid-/low-level cloud frequencies and precipitation decreases in the cold sector. This behavior seems to be related to a shift from stratiform to convective clouds and precipitation. Stronger ascent in the warm conveyor belt tends to enhance cloudiness and precipitation across the cold front. A strong temperature contrast between the warm and cold sectors also encourages greater post-cold-frontal cloud occurrence. While the seasonal contrasts in environmental temperature, moisture, and ascent strength are enough to explain most of the variations in cloud and precipitation across cold fronts in both hemispheres, they do not fully explain the differences between Northern and Southern Hemisphere cold fronts. These differences are better explained when the impact of the contrast in temperature across the cold front is also considered. In addition, these large-scale parameters do not explain the relatively large frequency in springtime postfrontal precipitation.

scholarly journals Exploring the microbiome in health and disease

2017 ◽  
Vol 1 ◽  
pp. 239784731774188 ◽  
Author(s):  
Elena Scotti ◽  
Stéphanie Boué ◽  
Giuseppe Lo Sasso ◽  
Filippo Zanetti ◽  
Vincenzo Belcastro ◽  
...  
Keyword(s):  
Human Health ◽  
Metabolic Diseases ◽  
Skin Diseases ◽  
Human Microbiome ◽  
Chronic Obstructive ◽  
Microbial Composition ◽  
Obstructive Pulmonary Disease ◽  
New Findings ◽  
Dynamics And Function ◽  
And Function

The analysis of human microbiome is an exciting and rapidly expanding field of research. In the past decade, the biological relevance of the microbiome for human health has become evident. Microbiome comprises a complex collection of microorganisms, with their genes and metabolites, colonizing different body niches. It is now well known that the microbiome interacts with its host, assisting in the bioconversion of nutrients and detoxification, supporting immunity, protecting against pathogenic microbes, and maintaining health. Remarkable new findings showed that our microbiome not only primarily affects the health and function of the gastrointestinal tract but also has a strong influence on general body health through its close interaction with the nervous system and the lung. Therefore, a perfect and sensitive balanced interaction of microbes with the host is required for a healthy body. In fact, growing evidence suggests that the dynamics and function of the indigenous microbiota can be influenced by many factors, including genetics, diet, age, and toxicological agents like cigarette smoke, environmental contaminants, and drugs. The disruption of this balance, that is called dysbiosis, is associated with a plethora of diseases, including metabolic diseases, inflammatory bowel disease, chronic obstructive pulmonary disease, periodontitis, skin diseases, and neurological disorders. The importance of the host microbiome for the human health has also led to the emergence of novel therapeutic approaches focused on the intentional manipulation of the microbiota, either by restoring missing functions or eliminating harmful roles. In the present review, we outline recent studies devoted to elucidate not only the role of microbiome in health conditions and the possible link with various types of diseases but also the influence of various toxicological factors on the microbial composition and function.

scholarly journals The Impact of Environmental Chemicals on the Gut Microbiome

2020 ◽  
Vol 176 (2) ◽  
pp. 253-284 ◽  
Author(s):  
Karen Chiu ◽  
Genoa Warner ◽  
Romana A Nowak ◽  
Jodi A Flaws ◽  
Wenyan Mei
Keyword(s):  
Gut Microbiome ◽  
Current Knowledge ◽  
Environmental Chemicals ◽  
Microbial Composition ◽  
Multiple Factors ◽  
Microbiome Research ◽  
Health Related ◽  
Exogenous Factors ◽  
The Impact ◽  
Insight Into

Abstract Since the surge of microbiome research in the last decade, many studies have provided insight into the causes and consequences of changes in the gut microbiota. Among the multiple factors involved in regulating the microbiome, exogenous factors such as diet and environmental chemicals have been shown to alter the gut microbiome significantly. Although diet substantially contributes to changes in the gut microbiome, environmental chemicals are major contaminants in our food and are often overlooked. Herein, we summarize the current knowledge on major classes of environmental chemicals (bisphenols, phthalates, persistent organic pollutants, heavy metals, and pesticides) and their impact on the gut microbiome, which includes alterations in microbial composition, gene expression, function, and health effects in the host. We then discuss health-related implications of gut microbial changes, which include changes in metabolism, immunity, and neurological function.

scholarly journals Exposure to airborne gold nanoparticles: a review of current toxicological data on the respiratory tract

2020 ◽  
Vol 22 (8) ◽  
Author(s):  
Barbara De Berardis ◽  
Magda Marchetti ◽  
Anna Risuglia ◽  
Federica Ietto ◽  
Carla Fanizza ◽  
...  
Keyword(s):  
Gold Nanoparticles ◽  
Human Health ◽  
Large Scale ◽  
Current Knowledge ◽  
Engineered Nanoparticles ◽  
In Vivo Studies ◽  
Field Exposure ◽  
The Impact

AbstractIn recent years, the introduction of innovative low-cost and large-scale processes for the synthesis of engineered nanoparticles with at least one dimension less than 100 nm has led to countless useful and extensive applications. In this context, gold nanoparticles stimulated a growing interest, due to their peculiar characteristics such as ease of synthesis, chemical stability and optical properties. This stirred the development of numerous applications especially in the biomedical field. Exposure of manufacturers and consumers to industrial products containing nanoparticles poses a potential risk to human health and the environment. Despite this, the precise mechanisms of nanomaterial toxicity have not yet been fully elucidated. It is well known that the three main routes of exposure to nanomaterials are by inhalation, ingestion and through the skin, with inhalation being the most common route of exposure to NPs in the workplace. To provide a complete picture of the impact of inhaled gold nanoparticles on human health, in this article, we review the current knowledge about the physico-chemical characteristics of this nanomaterial, in the size range of 1–100 nm, and its toxicity for pulmonary structures both in vitro and in vivo. Studies comparing the toxic effect of NPs larger than 100 nm (up to 250 nm) are also discussed.

scholarly journals Molecular Reconstruction of the Diet in Human Stool Samples

mSystems ◽  
2019 ◽  
Vol 4 (6) ◽  
Author(s):  
Frank Maixner
Keyword(s):  
Human Subjects ◽  
Human Microbiome ◽  
Microbial Composition ◽  
Microbiome Composition ◽  
Diet Surveys ◽  
Dna Metabarcoding ◽  
Microbiome Research ◽  
Dietary Records ◽  
Stool Samples ◽  
Chloroplast Dna Markers

ABSTRACT Understanding dietary effects on the gut microbial composition is one of the key questions in human microbiome research. It is highly important to have reliable dietary data on the stool samples to unambiguously link the microbiome composition to food intake. Often, however, self-reported diet surveys have low accuracy and can be misleading. Thereby, additional molecular biology-based methods could help to revise the diet composition. The article by Reese et al. [A. T. Reese, T. R. Kartzinel, B. L. Petrone, P. J. Turnbaugh, et al., mSystems 4(5):e00458-19, 2019, https://doi.org/10.1128/mSystems.00458-19] in a recent issue of mSystems describes a DNA metabarcoding strategy targeting chloroplast DNA markers in stool samples from 11 human subjects consuming both controlled and freely selected diets. The aim of this study was to evaluate the efficiency of this molecular method in detecting plant remains in the sample compared to the written dietary records. This study displays an important first step in implementing molecular dietary reconstructions in stool microbiome studies which will finally help to increase the accuracy of dietary metadata.

scholarly journals Methylmercury Impact on Adult Neurogenesis: Is the Worst Yet to Come From Recent Brazilian Environmental Disasters?

2020 ◽  
Vol 12 ◽  
Author(s):  
Ramon da Silva Raposo ◽  
Daniel Vieira Pinto ◽  
Ricardo Moreira ◽  
Ronaldo Pereira Dias ◽  
Carlos Alberto Fontes Ribeiro ◽  
...  
Keyword(s):  
Cognitive Decline ◽  
Human Health ◽  
Large Scale ◽  
Brain Aging ◽  
Adult Brain ◽  
Neurogenic Niche ◽  
Environmental Disasters ◽  
Neurodevelopmental Abnormalities ◽  
To Come ◽  
The Impact

Worldwide environmental tragedies of anthropogenic origin causing massive release of metals and other pollutants have been increasing considerably. These pollution outbreaks affect the ecosystems and impact human health. Among those tragedies, recent large-scale environmental disasters in Brazil strongly affected riverside populations, leading to high-risk exposure to methylmercury (MeHg). MeHg is highly neurotoxic to the developing brain. This toxicant causes neural stem cell dysfunction and neurodevelopmental abnormalities. However, less is known about the effects of MeHg in the postnatal neurogenic niche, which harbors neural stem cells and their progeny, in the adult brain. Therefore, taking in consideration the impact of MeHg in human health it is urgent to clarify possible associations between exposure to mercury, accelerated cognitive decline, and neurodegenerative diseases. In this perspectives paper, we discuss the neurotoxic mechanisms of MeHg on postnatal neurogenesis and the putative implications associated with accelerated brain aging and early-onset cognitive decline in populations highly exposed to this environmental neurotoxicant.

scholarly journals Unity of bowel-lung axis and the role of beneficial microbiota in anti-infectious protection

2021 ◽  
Vol 4 (4) ◽  
pp. 355-361
Author(s):  
T.E. Taranushenko ◽  
Keyword(s):  
Immune Responses ◽  
Respiratory Infections ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Medical Community ◽  
Mucosal Inflammation ◽  
Potential Interactions ◽  
The Impact ◽  
And Child Health

NIH Human Microbiome Project determined particular attention of the worldwide medical community to the study of the human microbiome and the assessment of the impact of symbiont microorganisms in the development of various (not only gastrointestinal) disorders. Potential interactions between the bowel and lungs (bowel-lung axis) via microbiota that allow for the possible involvement of microorganisms in the development of respiratory diseases are actively debated. This paper reviews studies on the pattern of interactions between bowel and lungs in infectious diseases associated with mucosal inflammation. The association between gut microbiota and the protective barrier of the respiratory tract based on known mechanisms and novel data derived from recent studies on SARS-CoV-2 is discussed. The relevance of beneficial bacteria (symbionts) in local and systemic immune responses, their disease-modifying and, eventually, therapeutic strategymodifying properties, the ability to be a resource of preventive medicine and an orchestrating tool for infections are addressed. Practitioners’ difficulties with probiotics in preventive and treatment schedules for various conditions are highlighted. Finally, the use of probiotics in children with respiratory infections and COVID-19 is uncovered. KEYWORDS: microbiota, microbiome, probiotics, children, mucosal immunity, Bifidobacterium. FOR CITATION: Taranushenko T.E. Unity of bowel-lung axis and the role of beneficial microbiota in anti-infectious protection. Russian Journal of Woman and Child Health. 2021;4(4):355–361 (in Russ.). DOI: 10.32364/2618-8430-2021-4-4-355-361.

scholarly journals Searching more genomic sequence with less memory for fast and accurate metagenomic profiling

2016 ◽  
Author(s):  
Shea N Gardner ◽  
Sasha K Ames ◽  
Maya B Gokhale ◽  
Tom R Slezak ◽  
Jonathan Allen
Keyword(s):  
Large Scale ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Low Cost ◽  
False Negative ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Metagenomic Data ◽  
Reference Database ◽  
Metagenomic Sequence

Software for rapid, accurate, and comprehensive microbial profiling of metagenomic sequence data on a desktop will play an important role in large scale clinical use of metagenomic data. Here we describe LMAT-ML (Livermore Metagenomics Analysis Toolkit-Marker Library) which can be run with 24 GB of DRAM memory, an amount available on many clusters, or with 16 GB DRAM plus a 24 GB low cost commodity flash drive (NVRAM), a cost effective alternative for desktop or laptop users. We compared results from LMAT with five other rapid, low-memory tools for metagenome analysis for 131 Human Microbiome Project samples, and assessed discordant calls with BLAST. All the tools except LMAT-ML reported overly specific or incorrect species and strain resolution of reads that were in fact much more widely conserved across species, genera, and even families. Several of the tools misclassified reads from synthetic or vector sequence as microbial or human reads as viral. We attribute the high numbers of false positive and false negative calls to a limited reference database with inadequate representation of known diversity. Our comparisons with real world samples show that LMAT-ML is the only tool tested that classifies the majority of reads, and does so with high accuracy.

scholarly journals A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases

2021 ◽  
Vol 118 (23) ◽  
pp. e2023202118
Author(s):  
Michael J. Tisza ◽  
Christopher B. Buck
Keyword(s):  
Human Health ◽  
Chronic Diseases ◽  
Sequence Data ◽  
Virus Disease ◽  
Case Control ◽  
Viral Sequence ◽  
Case Control Studies ◽  
Disease Associations ◽  
Microbiome Research ◽  
The Impact

Despite remarkable strides in microbiome research, the viral component of the microbiome has generally presented a more challenging target than the bacteriome. This gap persists, even though many thousands of shotgun sequencing runs from human metagenomic samples exist in public databases, and all of them encompass large amounts of viral sequence data. The lack of a comprehensive database for human-associated viruses has historically stymied efforts to interrogate the impact of the virome on human health. This study probes thousands of datasets to uncover sequences from over 45,000 unique virus taxa, with historically high per-genome completeness. Large publicly available case-control studies are reanalyzed, and over 2,200 strong virus–disease associations are found.

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