scholarly journals Forensic Human Identification for Cutaneous Microbiome, a Brief Review

2021 ◽  
Vol 10 (3) ◽  
pp. 244-251
Author(s):  
Natasha R.F. Novaes ◽  
Isabel C. M. Fensterseifer ◽  
José L. R. Martins ◽  
Osmar N. Silva
Keyword(s):  
Bacterial Genome ◽  
Human Microbiome ◽  
Human Identification ◽  
Human Microbiome Project ◽  
Forensic Identification ◽  
Skin Microbiome ◽  
Predictive Algorithms ◽  
Forensic Microbiology ◽  
The Relationship

Forensic Science compounds many study areas in context of solving crimes, one of which is the forensic microbiology. Combined with genomic approaches, microbiology has shown strong performance in studies regarding the relationship between microorganisms present on human skin and environment. The Human Microbiome Project (HMP) has contributed significantly to characterization of microbial complexity and their connection to human being. The purpose of this work consists of a historical overview of scientific articles, demonstrating the growth and possibility of using skin microbiome in forensic identification. Studies about use of cutaneous microbiome in human identification, as well its forensic approaches, were looked into for writing of this review. Comparisons among cutaneous microbial communities and manipulated objects have been tested using 16S rRNA, as well as a thorough sequencing of the bacterial genome. From use of ecological measures of distance to genetic markers with nucleotide variants and predictive algorithms, research has shown promising results for advances in field of forensic identification. The development of metagenomic microbial panel markers, named hidSkinPlax for targeted sequencing has been designed and tested with great results. Research results show satisfactory potential in human identification by cutaneous microbiome and the possibility for contributive use in elucidating crimes.

Integrating microbiome, transcriptome and metabolome data to investigate gastric disease pathogenesis: a concise review

2021 ◽  
Vol 23 ◽  
Author(s):  
Dalla Doohan ◽  
Yudith Annisa Ayu Rezkitha ◽  
Langgeng Agung Waskito ◽  
Ratha-korn Vilaichone ◽  
Yoshio Yamaoka ◽  
...  
Keyword(s):  
Human Microbiome ◽  
Human Microbiome Project ◽  
Gastric Disease ◽  
Disease Pathogenesis ◽  
Multiple Datasets ◽  
High Throughput Technology ◽  
Functional Profiling ◽  
Condition Indicator ◽  
The Relationship ◽  
Generation Sequencing

Abstract Microbiome, the study of microbial communities in specific environments, has developed significantly since the Human Microbiome Project began. Microbiomes have been associated with changes within environmental niches and the development of various diseases. The development of high-throughput technology such as next-generation sequencing has also allowed us to perform transcriptome studies, which provide accurate functional profiling data. Metabolome studies, which analyse the metabolites found in the environment, are the most direct environmental condition indicator. Although each dataset provides valuable information on its own, the integration of multiple datasets provides a deeper understanding of the relationship between the host, agent and environment. Therefore, network analysis using multiple datasets might give a clearer understanding of disease pathogenesis.

scholarly journals Improving characterization of understudied human microbiomes using targeted phylogenetics

2019 ◽  
Author(s):  
Bruce A Rosa ◽  
Kathie Mihindukulasuriya ◽  
Kymberlie Hallsworth-Pepin ◽  
Aye Wollam ◽  
John Martin ◽  
...  
Keyword(s):  
Human Microbiome ◽  
Human Microbiome Project ◽  
Genomic Sequences ◽  
Bacterial Strains ◽  
Bacterial Genomes ◽  
Genomic Databases ◽  
Disease States ◽  
Health And Disease ◽  
Taxonomic Groups

AbstractWhole genome bacterial sequences are required to better understand microbial functions, niches-pecific bacterial metabolism, and disease states. Although genomic sequences are available for many of the human-associated bacteria from commonly tested body habitats (e.g. stool), as few as 13% of bacterial-derived reads from other sites such as the skin map to known bacterial genomes. To facilitate a better characterization of metagenomic shotgun reads from under-represented body sites, we collected over 10,000 bacterial isolates originating from 14 human body habitats, identified novel taxonomic groups based on full length 16S rRNA sequences, clustered the sequences to ensure that no individual taxonomic group was over-selected for sequencing, prioritized bacteria from under-represented body sites (such as skin, respiratory and urinary tract), and sequenced and assembled genomes for 665 new bacterial strains. Here we show that addition of these genomes improved read mapping rates of HMP metagenomic samples by nearly 30% for the previously under-represented phylum Fusobacteria, and 27.5% of the novel genomes generated here had high representation in at least one of the tested HMP samples, compared to 12.5% of the sequences in the public databases, indicating an enrichment of useful novel genomic sequences resulting from the prioritization procedure. As our understanding of the human microbiome continues to improve and to enter the realm of therapy developments, targeted approaches such as this to improve genomic databases will increase in importance from both an academic and clinical perspective.ImportanceThe human microbiome plays a critically important role in health and disease, but current understanding of the mechanisms underlying the interactions between the varying microbiome and the different host environments is lacking. Having access to a database of fully sequenced bacterial genomes provides invaluable insights into microbial functions, but currently sequenced genomes for the human microbiome have largely come from a limited number of body sites (primarily stool), while other sites such as the skin, respiratory tract and urinary tracts are under-represented, resulting in as little as 13% of bacterial-derived reads mapping to known bacterial genomes. Here, we sequenced and assembled 665 new bacterial genomes, prioritized from a larger database to select under-represented body sites and bacterial taxa in the existing databases. As a result, we substantially improve mapping rates for samples from the Human Microbiome Project and provide an important contribution to human bacterial genomic databases for future studies.

scholarly journals Oral Microbiome and Cancer Therapy-Induced Oral Mucositis

2019 ◽  
Vol 2019 (53) ◽  
Author(s):  
Jean-Luc C Mougeot ◽  
Craig B Stevens ◽  
Darla S Morton ◽  
Michael T Brennan ◽  
Farah B Mougeot
Keyword(s):  
Cancer Therapy ◽  
Oral Mucositis ◽  
Human Microbiome ◽  
Holistic Approach ◽  
Human Microbiome Project ◽  
Oral Microbiome ◽  
Commensal Microbiota ◽  
Intestinal Mucositis

AbstractCharacterization of the role of oral microbiome in cancer therapy-induced oral mucositis (CTOM) is critical in preventing the clinically deleterious effects on patients’ health that are associated with CTOM. Funding initiatives related to the National Institutes of Health human microbiome project have resulted in groundbreaking advancements in biology and medicine during the last decade. These advancements have shown that a human being is in fact a superorganism made of human cells and associated symbiotic or commensal microbiota. In this review, we describe the state of science as it relates to fundamental knowledge on oral microbiome and its role in CTOM. We also discuss how state-of-the-art technologies and systems biology tools may be used to help tackle the difficult challenges ahead to develop effective treatments or preventive therapies for oral mucositis. We make a clear distinction between disease processes pertaining to the oral microbiome, which includes opportunistic pathogens that may be defined as pathobionts, and those infectious disease processes initiated by exogenous pathogens. We also explored the extent to which knowledge from the gastrointestinal tract in disease and intestinal mucositis could help us better understand CTOM pathobiology. Finally, we propose a model in which the oral microbiome participates in the current five-step CTOM pathobiology model. With the advent of more sophisticated metagenomics technologies and methods of analysis, much hope lies ahead to implement an effective holistic approach to treat cancer patients affected by CTOM.

scholarly journals Strains, functions and dynamics in the expanded Human Microbiome Project

Nature ◽  
2017 ◽  
Vol 550 (7674) ◽  
pp. 61-66 ◽  
Author(s):  
Jason Lloyd-Price ◽  
Anup Mahurkar ◽  
Gholamali Rahnavard ◽  
Jonathan Crabtree ◽  
Joshua Orvis ◽  
...  
Keyword(s):  
Human Microbiome ◽  
Human Microbiome Project ◽  
Temporal Analysis ◽  
National Institutes Of Health ◽  
Strain Identification ◽  
Multiple Time ◽  
Functional Profiling ◽  
Multiple Time Points ◽  
Second Wave

Abstract The characterization of baseline microbial and functional diversity in the human microbiome has enabled studies of microbiome-related disease, diversity, biogeography, and molecular function. The National Institutes of Health Human Microbiome Project has provided one of the broadest such characterizations so far. Here we introduce a second wave of data from the study, comprising 1,631 new metagenomes (2,355 total) targeting diverse body sites with multiple time points in 265 individuals. We applied updated profiling and assembly methods to provide new characterizations of microbiome personalization. Strain identification revealed subspecies clades specific to body sites; it also quantified species with phylogenetic diversity under-represented in isolate genomes. Body-wide functional profiling classified pathways into universal, human-enriched, and body site-enriched subsets. Finally, temporal analysis decomposed microbial variation into rapidly variable, moderately variable, and stable subsets. This study furthers our knowledge of baseline human microbial diversity and enables an understanding of personalized microbiome function and dynamics.

scholarly journals Improving Characterization of Understudied Human Microbiomes Using Targeted Phylogenetics

mSystems ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Bruce A. Rosa ◽  
Kathie Mihindukulasuriya ◽  
Kymberlie Hallsworth-Pepin ◽  
Aye Wollam ◽  
John Martin ◽  
...  
Keyword(s):  
Human Microbiome ◽  
Human Microbiome Project ◽  
Genomic Sequences ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Bacterial Genomes ◽  
Genomic Databases ◽  
Disease States ◽  
Taxonomic Groups

ABSTRACT Whole-genome bacterial sequences are required to better understand microbial functions, niche-specific bacterial metabolism, and disease states. Although genomic sequences are available for many of the human-associated bacteria from commonly tested body habitats (e.g., feces), as few as 13% of bacterium-derived reads from other sites such as the skin map to known bacterial genomes. To facilitate a better characterization of metagenomic shotgun reads from underrepresented body sites, we collected over 10,000 bacterial isolates originating from 14 human body habitats, identified novel taxonomic groups based on full-length 16S rRNA gene sequences, clustered the sequences to ensure that no individual taxonomic group was overselected for sequencing, prioritized bacteria from underrepresented body sites (such as skin and respiratory and urinary tracts), and sequenced and assembled genomes for 665 new bacterial strains. Here, we show that addition of these genomes improved read mapping rates of Human Microbiome Project (HMP) metagenomic samples by nearly 30% for the previously underrepresented phylum Fusobacteria, and 27.5% of the novel genomes generated here had high representation in at least one of the tested HMP samples, compared to 12.5% of the sequences in the public databases, indicating an enrichment of useful novel genomic sequences resulting from the prioritization procedure. As our understanding of the human microbiome continues to improve and to enter the realm of therapy developments, targeted approaches such as this to improve genomic databases will increase in importance from both an academic and a clinical perspective. IMPORTANCE The human microbiome plays a critically important role in health and disease, but current understanding of the mechanisms underlying the interactions between the varying microbiome and the different host environments is lacking. Having access to a database of fully sequenced bacterial genomes provides invaluable insights into microbial functions, but currently sequenced genomes for the human microbiome have largely come from a limited number of body sites (primarily feces), while other sites such as the skin, respiratory tract, and urinary tract are underrepresented, resulting in as little as 13% of bacterium-derived reads mapping to known bacterial genomes. Here, we sequenced and assembled 665 new bacterial genomes, prioritized from a larger database to select underrepresented body sites and bacterial taxa in the existing databases. As a result, we substantially improve mapping rates for samples from the Human Microbiome Project and provide an important contribution to human bacterial genomic databases for future studies.

scholarly journals Microbiome and Cancer Immunotherapy

2021 ◽  
Vol 96 (4) ◽  
pp. 312-317
Author(s):  
Moonki Hong ◽  
Minkyu Jung
Keyword(s):  
Checkpoint Inhibitors ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Clinical Results ◽  
Genome Project ◽  
Human Diseases ◽  
The Past ◽  
Preclinical And Clinical Studies ◽  
Tumor Types ◽  
The Relationship

Immune checkpoint inhibitors (ICIs) have achieved promising clinical results in cancer treatment over the past decade. However, the efficacy of ICIs is less than 30% in most tumor types, and studies are underway to identify the predictive factors responsive to ICIs. More than 1,000 species of microorganisms live in the human body, and the second human genome project, The Human Microbiome Project, has been conducted to understand human diseases through interactions with microbes. As the microbiome project has progressed, many studies have reported on the association between microorganisms and human diseases, including preclinical and clinical studies on the relationship between ICIs and the microbiome. Therefore, in this manuscript, the relationship between the microbiome and cancer, especially the effectiveness of ICIs, is reviewed.

Skeletal elements of crinoid echinoderms: High-resolution structural and microanalytical results

1983 ◽  
Vol 41 ◽  
pp. 194-195
Author(s):  
D. F. Blake ◽  
L. F. Allard ◽  
D. R. Peacor
Keyword(s):  
High Resolution ◽  
Marine Invertebrates ◽  
Sea Urchins ◽  
Structural Features ◽  
Sea Stars ◽  
High Resolution Tem ◽  
Relationship Of ◽  
The Relationship ◽  
Insight Into

Echinodermata is a phylum of marine invertebrates which has been extant since Cambrian time (c.a. 500 m.y. before the present). Modern examples of echinoderms include sea urchins, sea stars, and sea lilies (crinoids). The endoskeletons of echinoderms are composed of plates or ossicles (Fig. 1) which are with few exceptions, porous, single crystals of high-magnesian calcite. Despite their single crystal nature, fracture surfaces do not exhibit the near-perfect {10.4} cleavage characteristic of inorganic calcite. This paradoxical mix of biogenic and inorganic features has prompted much recent work on echinoderm skeletal crystallography. Furthermore, fossil echinoderm hard parts comprise a volumetrically significant portion of some marine limestones sequences. The ultrastructural and microchemical characterization of modern skeletal material should lend insight into: 1). The nature of the biogenic processes involved, for example, the relationship of Mg heterogeneity to morphological and structural features in modern echinoderm material, and 2). The nature of the diagenetic changes undergone by their ancient, fossilized counterparts. In this study, high resolution TEM (HRTEM), high voltage TEM (HVTEM), and STEM microanalysis are used to characterize tha ultrastructural and microchemical composition of skeletal elements of the modern crinoid Neocrinus blakei.

Microstructural Characterization of Au-Ge-Ni based ohmic contacts to GaAs/AlGaAs modfet device

1987 ◽  
Vol 45 ◽  
pp. 326-327
Author(s):  
A.K. Rai ◽  
A.K. Petford-Long ◽  
A. Ezis ◽  
D.W. Langer
Keyword(s):  
Contact Resistance ◽  
Ohmic Contact ◽  
Ohmic Contacts ◽  
Microstructural Characterization ◽  
Almost Everywhere ◽  
Spacer Layer ◽  
Good Contact ◽  
The Relationship ◽  
Lower Contact

Considerable amount of work has been done in studying the relationship between the contact resistance and the microstructure of the Au-Ge-Ni based ohmic contacts to n-GaAs. It has been found that the lower contact resistivity is due to the presence of Ge rich and Au free regions (good contact area) in contact with GaAs. Thus in order to obtain an ohmic contact with lower contact resistance one should obtain a uniformly alloyed region of good contact areas almost everywhere. This can possibly be accomplished by utilizing various alloying schemes. In this work microstructural characterization, employing TEM techniques, of the sequentially deposited Au-Ge-Ni based ohmic contact to the MODFET device is presented.The substrate used in the present work consists of 1 μm thick buffer layer of GaAs grown on a semi-insulating GaAs substrate followed by a 25 Å spacer layer of undoped AlGaAs.

Characterization of Auditory Disability and Its Relation to the Resilience

2018 ◽  
Vol 5 (2) ◽  
pp. 15
Author(s):  
Bibian Bibeca Bumbila García ◽  
Hernán Andrés Cedeño Cedeño ◽  
Tatiana Moreira Chica ◽  
Yaritza Rossana Parrales Ríos
Keyword(s):  
Social Integration ◽  
Conceptual Analysis ◽  
Disabled People ◽  
Disabled Students ◽  
Hearing Disability ◽  
Technical University ◽  
The Relationship ◽  
Made In

The objective of the work is to establish the characterization of the auditory disability and its relationship with resilience at the Technical University of Manabí. The article shows a conceptual analysis related to the inclusion and social integration of disabled students. Based on the fact that the person with disabilities grows and develops in the same way as that of people without disabilities and what usually happens is that disabled people are rejected and discriminated against based on a prefabricated and erroneous conceptualization of these people. The results associated with the application of the SV-RES test prepared by the researchers are shown (Saavedra & Villalta, 2008b). Characterization of the auditory deficit is made in the students, and the limitations that derive from it are pointed out. We analyze the particularities related to communication with students who have a hearing disability and resilience in this type of student, where some personal highlights that in this sense constitute an example of resilience. Finally, the results related to the study of the relationship between students' hearing disability and the level of resilience dimensions are shown.

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