scholarly journals Biases in Viral Metagenomics-Based Detection, Cataloguing and Quantification of Bacteriophage Genomes in Human Faeces, a Review

2021 ◽  
Vol 9 (3) ◽  
pp. 524
Author(s):  
Julie Callanan ◽  
Stephen R. Stockdale ◽  
Andrey Shkoporov ◽  
Lorraine A. Draper ◽  
R. Paul Ross ◽  
...  
Keyword(s):  
Human Microbiome ◽  
Viral Metagenomics ◽  
Human Gut ◽  
Human Faeces ◽  
Vast Array ◽  
Viral Component ◽  
And Function ◽  
Bacterial Constituents

The human gut is colonised by a vast array of microbes that include bacteria, viruses, fungi, and archaea. While interest in these microbial entities has largely focused on the bacterial constituents, recently the viral component has attracted more attention. Metagenomic advances, compared to classical isolation procedures, have greatly enhanced our understanding of the composition, diversity, and function of viruses in the human microbiome (virome). We highlight that viral extraction methodologies are crucial in terms of identifying and characterising communities of viruses infecting eukaryotes and bacteria. Different viral extraction protocols, including those used in some of the most significant human virome publications to date, have introduced biases affecting their a overall conclusions. It is important that protocol variations should be clearly highlighted across studies, with the ultimate goal of identifying and acknowledging biases associated with different protocols and, perhaps, the generation of an unbiased and standardised method for examining this portion of the human microbiome.

scholarly journals Microbial Species that Initially Colonize the Human Gut at Birth or in Early Childhood Can Stay in Human Body for Lifetime

2021 ◽  
Author(s):  
Weizhong Li ◽  
Karen E. Nelson
Keyword(s):  
Early Childhood ◽  
Human Body ◽  
Rare Variants ◽  
Human Microbiome ◽  
Sample Collection ◽  
Human Gut ◽  
Significant Difference ◽  
And Function ◽  
Changes Over Time ◽  
Prevalent Species

AbstractIn recent years, many studies have described the composition and function of the human microbiome at different body sites and suggested a role for the microbiome in various diseases and health conditions. Some studies, using longitudinal samples, have also suggested how the microbiome changes over time due to disease, diet, development, travel, and other environmental factors. However, to date, no study has demonstrated whether the microorganisms established at birth or in early childhood, either transmitted from parents or obtained from the environment, can stay in the human body until adult or senior age. To directly answer this question is difficult, because microbiome samples at childhood and at later adulthood for the same individual will need to be compared and the field is not old enough to have allowed for that type of sample collection. Here, using a metagenomic approach, we analyzed 1004 gut microbiome samples from senior adults (65 ± 7.8 years) from the TwinsUK cohort. Our data indicate that many species in the human gut acquired in early childhood can stay for a lifetime until senior ages. We identified the rare genomic variants (single nucleotide variation and indels) for 27 prevalent species with enough sequencing coverage for confident genomic variant identification. We found that for some species, twin pairs, including both monozygotic (MZ) and dizygotic (DZ) twins, share significantly more rare variants than unrelated subject pairs. But no significant difference is found between MZ and DZ twin pairs. These observations strongly suggest that these species acquired in early childhood remained in these persons until senior adulthood.

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 Glycine Lipids ofBacteroides thetaiotaomicronAre Important for Fitness during GrowthIn VivoandIn Vitro

2018 ◽  
Vol 85 (10) ◽  
Author(s):  
Alli Lynch ◽  
Seshu R. Tammireddy ◽  
Mary K. Doherty ◽  
Phillip D. Whitfield ◽  
David J. Clarke
Keyword(s):  
Amino Acid ◽  
Gut Microbiome ◽  
Molecular Mechanisms ◽  
Cellular Membrane ◽  
Bacteroides Thetaiotaomicron ◽  
Human Gut ◽  
Acyltransferase Activity ◽  
Content Type ◽  
Health And Disease ◽  
And Function

ABSTRACTAcylated amino acids function as important components of the cellular membrane in some bacteria. Biosynthesis is initiated by theN-acylation of the amino acid, and this is followed by subsequentO-acylation of the acylated molecule, resulting in the production of the mature diacylated amino acid lipid. In this study, we use both genetics and liquid chromatography-mass spectrometry (LC-MS) to characterize the biosynthesis and function of a diacylated glycine lipid (GL) species produced inBacteroides thetaiotaomicron. We, and others, have previously reported the identification of a gene, namedglsBin this study, that encodes anN-acyltransferase activity responsible for the production of a monoacylated glycine calledN-acyl-3-hydroxy-palmitoyl glycine (or commendamide). In all of theBacteroidalesgenomes sequenced so far, theglsBgene is located immediately downstream from a gene, namedglsA, that is also predicted to encode a protein with acyltransferase activity. We use LC-MS to show that the coexpression ofglsBandglsAresults in the production of GL inEscherichia coli. We constructed a deletion mutant of theglsBgene inB. thetaiotaomicron, and we confirm thatglsBis required for the production of GL inB. thetaiotaomicron. Moreover, we show thatglsBis important for the ability ofB. thetaiotaomicronto adapt to stress and colonize the mammalian gut. Therefore, this report describes the genetic requirements for the biosynthesis of GL, a diacylated amino acid species that contributes to fitness in the human gut bacteriumB. thetaiotaomicron.IMPORTANCEThe gut microbiome has an important role in both health and disease of the host. The mammalian gut microbiome is often dominated by bacteria from theBacteroidales, an order that includesBacteroidesandPrevotella. In this study, we have identified an acylated amino acid, called glycine lipid, produced byBacteroides thetaiotaomicron, a beneficial bacterium originally isolated from the human gut. In addition to identifying the genes required for the production of glycine lipids, we show that glycine lipids have an important role during the adaptation ofB. thetaiotaomicronto a number of environmental stresses, including exposure to either bile or air. We also show that glycine lipids are important for the normal colonization of the murine gut byB. thetaiotaomicron. This work identifies glycine lipids as an important fitness determinant inB. thetaiotaomicronand therefore increases our understanding of the molecular mechanisms underpinning colonization of the mammalian gut by beneficial bacteria.

scholarly journals Revealing Protein-Level Functional Redundancy in the Human Gut Microbiome using Ultra-deep Metaproteomics

2021 ◽  
Author(s):  
Leyuan Li ◽  
Zhibin Ning ◽  
Xu Zhang ◽  
James Butcher ◽  
Caitlin Simopoulos ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Protein Level ◽  
Functional Organization ◽  
Human Microbiome ◽  
Functional Redundancy ◽  
Human Gut ◽  
Functional Roles ◽  
Human Gut Microbiome ◽  
Metagenomics Data ◽  
Network Approaches

Functional redundancy is a key property of ecosystems and represents the fact that phylogenetically unrelated taxa can play similar functional roles within an ecosystem. The redundancy of potential functions of human microbiome has been recently quantified using metagenomics data. Yet, the redundancy of functions which are actually expressed within the human microbiome remains largely unexplored. Here, we quantify the protein-level functional redundancy in the human gut microbiome using metaproteomics and network approaches. In particular, our ultra-deep metaproteomics approach revealed high protein-level functional redundancy and high nestedness in proteomic content networks - bipartite graphs that connect taxa with their expressed functions. We further examined multiple metaproteomics datasets and showed that various environmental factors, including individuality, biogeography, xenobiotics, and disease, significantly altered the protein-level functional redundancy. Finally, by projecting the bipartite proteomic content networks into unipartite weighted genus networks, functional hub genera across individual microbiomes were discovered, suggesting that there may be a universal principle of functional organization in microbiome assembly.

scholarly journals The Cultural Significance in Greeting Practices in Belo Dialect of the Bima Language

2019 ◽  
Vol 12 (2) ◽  
pp. 206-234
Author(s):  
Alek Alek
Keyword(s):  
National Language ◽  
Cultural Significance ◽  
Cultural Groups ◽  
Men And Women ◽  
Vast Array ◽  
Personal Names ◽  
Daily Interactions ◽  
And Function ◽  
Local Languages

Indonesia is the home to a vast array of cultures and many unique languages that are the mother tongues of these various islands and cultural groups. One of these is Bima language. Greeting systems and the address of personal names has long been a question of great interest in linguistic fields, especially sociolinguistic study. The main objective of the recent study was to answer some of the main issues as follows: (1) What are name variations in the greeting practices using in the Bima language? (2) How are the name variations applied in daily interactions of the Bima language? (3) Which syllables which are dominantly chosen in greeting terms? The results of my research will present the variations in the greeting system and address of personal names and their variety. Those variations are either at the beginning, the middle or the end of the syllables. However, none of the Bima people’s names begin with a consonant: “C, P, V, and X” as well as the vowel O.” it will also show that the variation of greeting practices and address of names applied in the daily interactions of the Bima language are different for men and women. The effort of maintaining the local style is essential to preserving and investigating as part of the national language because the position and function of the local languages are significant to the contribution and the progress and standardization of the national language. Keywords: Greeting practices, Bima language, and cultural significance

3. Proteins

2021 ◽  
pp. 34-51
Author(s):  
Mark Lorch
Keyword(s):  
Amino Acids ◽  
Protein Folding ◽  
Protein Structure ◽  
Protein Structures ◽  
Structure And Function ◽  
Vast Array ◽  
A Cell ◽  
Cellular Machinery ◽  
And Function ◽  
The Relationship

This chapter examines proteins, the dominant proportion of cellular machinery, and the relationship between protein structure and function. The multitude of biological processes needed to keep cells functioning are managed in the organism or cell by a massive cohort of proteins, together known as the proteome. The twenty amino acids that make up the bulk of proteins produce the vast array of protein structures. However, amino acids alone do not provide quite enough chemical variety to complete all of the biochemical activity of a cell, so the chapter also explores post-translation modifications. It finishes by looking as some dynamic aspects of proteins, including enzyme kinetics and the protein folding problem.

scholarly journals A Distinct Contractile Injection System Gene Cluster Found in a Majority of Healthy Adult Human Microbiomes

mSystems ◽  
2020 ◽  
Vol 5 (4) ◽  
Author(s):  
Maria I. Rojas ◽  
Giselle S. Cavalcanti ◽  
Katelyn McNair ◽  
Sean Benler ◽  
Amanda T. Alker ◽  
...  
Keyword(s):  
Inflammatory Bowel Disease ◽  
Gene Cluster ◽  
Bowel Disease ◽  
Human Microbiome ◽  
Gene Clusters ◽  
The United States ◽  
Injection System ◽  
Human Gut ◽  
Human Host ◽  
Inflammatory Bowel

ABSTRACT Many commensal bacteria antagonize each other or their host by producing syringe-like secretion systems called contractile injection systems (CIS). Members of the Bacteroidales family have been shown to produce only one type of CIS—a contact-dependent type 6 secretion system that mediates bacterium-bacterium interactions. Here, we show that a second distinct cluster of genes from Bacteroidales bacteria from the human microbiome may encode yet-uncharacterized injection systems that we term Bacteroidales injection systems (BIS). We found that BIS genes are present in the gut microbiomes of 99% of individuals from the United States and Europe and that BIS genes are more prevalent in the gut microbiomes of healthy individuals than in those individuals suffering from inflammatory bowel disease. Gene clusters similar to that of the BIS mediate interactions between bacteria and diverse eukaryotes, like amoeba, insects, and tubeworms. Our findings highlight the ubiquity of the BIS gene cluster in the human gut and emphasize the relevance of the gut microbiome to the human host. These results warrant investigations into the structure and function of the BIS and how they might mediate interactions between Bacteroidales bacteria and the human host or microbiome. IMPORTANCE To engage with host cells, diverse pathogenic bacteria produce syringe-like structures called contractile injection systems (CIS). CIS are evolutionarily related to the contractile tails of bacteriophages and are specialized to puncture membranes, often delivering effectors to target cells. Although CIS are key for pathogens to cause disease, paradoxically, similar injection systems have been identified within healthy human microbiome bacteria. Here, we show that gene clusters encoding a predicted CIS, which we term Bacteroidales injection systems (BIS), are present in the microbiomes of nearly all adult humans tested from Western countries. BIS genes are enriched within human gut microbiomes and are expressed both in vitro and in vivo. Further, a greater abundance of BIS genes is present within healthy gut microbiomes than in those humans with with inflammatory bowel disease (IBD). Our discovery provides a potentially distinct means by which our microbiome interacts with the human host or its microbiome.

scholarly journals Development of a Humanized Murine Model for the Study of Oxalobacter formigenes Intestinal Colonization

2019 ◽  
Vol 220 (11) ◽  
pp. 1848-1858 ◽  
Author(s):  
Amanda M Pebenito ◽  
Menghan Liu ◽  
Lama Nazzal ◽  
Martin J Blaser
Keyword(s):  
Kidney Stones ◽  
Human Microbiome ◽  
Epidemiological Studies ◽  
Microbial Populations ◽  
Murine Models ◽  
Oxalobacter Formigenes ◽  
Human Species ◽  
Human Gut ◽  
Germ Free ◽  
Β Diversity

Abstract Background Oxalobacter formigenes are bacteria that colonize the human gut and degrade oxalate, a component of most kidney stones. Findings of clinical and epidemiological studies suggest that O. formigenes colonization reduces the risk for kidney stones. We sought to develop murine models to allow investigating O. formigenes in the context of its native human microbiome. Methods For humanization, we transplanted pooled feces from healthy, noncolonized human donors supplemented with a human O. formigenes strain into recipient mice. We transplanted microbiota into mice that were treated with broad-spectrum antibiotics to suppress their native microbiome, were germ free, or received humanization without pretreatment or received sham gavage (controls). Results All humanized mice were stably colonized with O. formigenes through 8 weeks after gavage, whereas mice receiving sham gavage remained uncolonized (P < .001). Humanization significantly changed the murine intestinal microbial community structure (P < .001), with humanized germ-free and antibiotic-treated groups overlapping in β-diversity. Both germ-free and antibiotic-treated mice had significantly increased numbers of human species compared with sham-gavaged mice (P < .001). Conclusions Transplanting mice with human feces and O. formigenes introduced new microbial populations resembling the human microbiome, with stable O. formigenes colonization; such models can define optimal O. formigenes strains to facilitate clinical trials.

scholarly journals The Gut Microbiome as a Component of the Gut–Brain Axis in Cognitive Health

2020 ◽  
Vol 22 (4) ◽  
pp. 485-494
Author(s):  
Wen Gao ◽  
Kelley L. Baumgartel ◽  
Sheila A. Alexander
Keyword(s):  
Cognitive Development ◽  
Gut Microbiome ◽  
Human Microbiome ◽  
Vital Role ◽  
The Body ◽  
Nursing Research ◽  
Brain Physiology ◽  
Cognitive States ◽  
And Function ◽  
Development Stability

Introduction: The human microbiome, the microorganisms living in and on the body, plays a vital role in brain physiology and pathophysiology. The gut microbiome (GMB) has been identified as a link in the gut–brain axis moderating cognitive development and health. Objectives: The objectives of this scoping review are to discuss mechanisms of the microbiome–gut–brain axis in cognition, review the existing literature on the GMB and cognition, and discuss implications for nursing research. Methods: We searched Pubmed using the terms “gut microbiome,” “brain,” and “cognition” and the terms “gut brain axis,” “microbiome,” and “cognition”; removed duplicates, studies not published in English, and unrelated publications; and added additional articles identified through references. We retained the 85 most relevant publications for this review. Results: Common themes in the current literature include GMB components; interactions on cognitive development; effects of GMB–gut–brain interactions on cognition, mild cognitive impairment and Alzheimer’s disease; effects of GMB interactions with physiologic stress on cognition in critical care; and GMB modification for improved cognition. Review of the literature on each of these topics reveals multiple theoretical mechanisms of action for GMB–gut–brain interaction that modify cognitive development and function across the lifespan. Discussion: GMB components and dysbiosis have been implicated in many cognitive states, and specific microbiota constituents contribute to cognitive development, stability, and impairment. The study of these interactions is relevant to nursing research as it addresses the holistic human experience and microbiome constituents are modifiable, facilitating translation into the clinical setting.

scholarly journals Insights into the structure and function of HV1 from a meta-analysis of mutation studies

2016 ◽  
Vol 148 (2) ◽  
pp. 97-118 ◽  
Author(s):  
Thomas E. DeCoursey ◽  
Deri Morgan ◽  
Boris Musset ◽  
Vladimir V. Cherny
Keyword(s):  
Amino Acid ◽  
Ion Channel ◽  
Meta Analysis ◽  
Structure And Function ◽  
Proton Channel ◽  
Vast Array ◽  
Voltage Gated ◽  
Interspecies Differences ◽  
And Function ◽  
Sheer Number

The voltage-gated proton channel (HV1) is a widely distributed, proton-specific ion channel with unique properties. Since 2006, when genes for HV1 were identified, a vast array of mutations have been generated and characterized. Accessing this potentially useful resource is hindered, however, by the sheer number of mutations and interspecies differences in amino acid numbering. This review organizes all existing information in a logical manner to allow swift identification of studies that have characterized any particular mutation. Although much can be gained from this meta-analysis, important questions about the inner workings of HV1 await future revelation.

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