broken links clinical-and-public-health-microbiology – .

Nice bacteria finish last – resistant bacteria help their kin survive antibiotics, but at a cost

the link https://micronow.org/cohabiting-couples-have-similar-microbiomes/ will likely not function for very long after — 08.22.2017

PROBLEM LINK * Meet the Scientist #43 - Rob Knight: The Microbes That Inhabit Us – Knight studies our inner ecology: the 100 trillion microbes that grow in and on our bodies. Knight explained how hundreds of species can coexist on the palm of your hand, how bacteria manipulate your immune system and maybe even your brain, and how obesity and other health problems may come down to the wrong balance of microbes. leads to website micronow home, not Rob Knight's article

Hamilton, ON (August 31, 2011) - Scientists were surprised at how fast bacteria developed resistance to the miracle antibiotic drugs when they were developed less than a century ago. Now scientists at McMaster University have found that resistance has been around for at least 30,000 years.

Human skin harbours unknown bugs Staphylococcus aureus Staphylococcus bacteria are commonly found on the skin Human skin is a “virtual zoo” of bacteria, say researchers who have identified more than 200 species in samples taken from the forearm. Study leader Professor Martin Blaser

17 November 2010 Life is found in deepest layer of Earth’s crust By Michael Marshall

Legacy content e79 e89



Update Fierer: Science. 2009 May 29;324(5931):1190-2. Topographical and temporal diversity of the human skin microbiome. Grice EA, Kong HH, Conlan S, Deming CB, Davis J, Young AC; NISC Comparative Sequencing Program, Bouffard GG, Blakesley RW, Murray PR, Green ED, Turner ML, Segre JA. Genetics and Molecular Biology Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA. Comment in: Science. 2009 Aug 21;325(5943):944-5. Abstract Human skin is a large, heterogeneous organ that protects the body from pathogens while sustaining microorganisms that influence human health and disease. Our analysis of 16S ribosomal RNA gene sequences obtained from 20 distinct skin sites of healthy humans revealed that physiologically comparable sites harbor similar bacterial communities. The complexity and stability of the microbial community are dependent on the specific characteristics of the skin site. This topographical and temporal survey provides a baseline for studies that examine the role of bacterial communities in disease states and the microbial interdependencies required to maintain healthy skin. PMID: 19478181

http://www.nature.com/news/2010/100714/full/news.2010.353.html “microbiologists have discovered new viral genes in faeces. They find that the composition of virus populations inhabiting the tail ends of healthy intestines (as represented in our stools) is unique to each individual and stable over time. Even identical twins who share many of the same intestinal bacteria differed in their gut's viral make-up” ..Trevor..

BMC Genomics. 2010 Sep 7;11:488. Molecular analysis of the diversity of vaginal microbiota associated with bacterial vaginosis.69) Ling Z, Kong J, Liu F, Zhu H, Chen X, Wang Y, Li L, Nelson KE, Xia Y, Xiang C. State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China. Abstract BACKGROUND: Bacterial vaginosis (BV) is an ecological disorder of the vaginal microbiota that affects millions of women annually, and is associated with numerous adverse health outcomes including pre-term birth and the acquisition of sexually transmitted infections. However, little is known about the overall structure and composition of vaginal microbial communities; most of the earlier studies focused on predominant vaginal bacteria in the process of BV. In the present study, the diversity and richness of vaginal microbiota in 50 BV positive and 50 healthy women from China were investigated using culture-independent PCR-denaturing gradient gel electrophoresis (DGGE) and barcoded 454 pyrosequencing methods, and validated by quantitative PCR. RESULTS: Our data demonstrated that there was a profound shift in the absolute and relative abundances of bacterial species present in the vagina when comparing populations associated with healthy and diseased conditions. In spite of significant interpersonal variations, the diversity of vaginal microbiota in the two groups could be clearly divided into two clusters. A total of 246,359 high quality pyrosequencing reads was obtained for evaluating bacterial diversity and 24,298 unique sequences represented all phylotypes. The most predominant phyla of bacteria identified in the vagina belonged to Firmicutes, Bacteroidetes, Actinobacteria and Fusobacteria. The higher number of phylotypes in BV positive women over healthy is consistent with the results of previous studies and a large number of low-abundance taxa which were missed in previous studies were revealed. Although no single bacterium could be identified as a specific marker for healthy over diseased conditions, three phyla - Bacteroidetes, Actinobacteria and Fusobacteria, and eight genera including Gardnerella, Atopobium, Megasphaera, Eggerthella, Aerococcus, Leptotrichia/Sneathia, Prevotella and Papillibacter were strongly associated with BV (p < 0.05). These genera are potentially excellent markers and could be used as targets for clinical BV diagnosis by molecular approaches. CONCLUSIONS: The data presented here have clearly profiled the overall structure of vaginal communities and clearly demonstrated that BV is associated with a dramatic increase in the taxonomic richness and diversity of vaginal microbiota. The study also provides the most comprehensive picture of the vaginal community structure and the bacterial ecosystem, and significantly contributes to the current understanding of the etiology of BV. PMID: 20819230

Mycobacteria inhibition of IFN-gamma induced HLA-DR gene expression by up-regulating histone deacetylation at the promoter region in human THP-1 monocytic cells70) Infection of macrophages with mycobacteria has been shown to inhibit the macrophage response to IFN-gamma. In the current study, we examined the effect of Mycobacteria avium, Mycobacteria tuberculosis, and TLR2A receptor which is expressed on the surface of certain cells and recognizes native or foreign substances and passes on appropriate signals to the cell and/or the nervous system. stimulation on IFN-gamma-induced gene expression in human PMA-differentiated THP-1 monocytic cells. Mycobacterial infection inhibited IFN-gamma-induced expression of HLA-DRalpha and HLA-DRbeta mRNA and partially inhibited CIITA expression but did not affect expression of IFN regulatory factor-1 mRNA. To determine whether inhibition of histone deacetylase (HDAC) activity could rescue HLA-DR gene expression, butyric acid and MS-275, inhibitors of HDAC activity, were added at the time of M. avium or M. tuberculosis infection or TLR2 stimulation. HDAC inhibition restored the ability of these cells to express HLA-DRalpha and HLA-DRbeta mRNA in response to IFN-gamma. Histone acetylation induced by IFN-gamma at the HLA-DRalpha promoter was repressed upon mycobacteria infection or TLR2 stimulation. HDAC gene expression was not affected by mycobacterial infection. However, mycobacterial infection or TLR2 stimulation up-regulated expression of mammalian Sin3A, a corepressor that is required for MHC class II repression by HDAC. Furthermore, we show that the mammalian Sin3A corepressor is associated with the HLA-DRalpha promoter in M. avium-infected THP-1 cells stimulated with IFN-gamma. Thus, mycobacterial infection of human THP-1 cells specifically inhibits HLA-DR gene expression by a novel pathway that involves HDAC complex formation at the HLA-DR promoter, resulting in histone deacetylation and gene silencing. Trevor? - “Crafty little buggers indeed! So what this is saying is that the mycobacteria are able to silence genes associated with the immune systems ability to react to infection by increasing HDAC. The use of HDAC inhibitors in culture lead to the clearance of recalcitrant intracellular bacterial infections. However, the use of HDAC inhibitors can lead to viremia as the body also uses HDAC to silence cellular machinary associated with viral replication as the HDAC inhibitors are non-specific in their action. Its a Catch22.”

Joyce,Good point. Helicobacter pylori were recently found circulating in peripheral blood, showing that the GI tract is not so well isolated from the rest of the body as had previously been believed. I think the gut flora is key to introduction of new species to our systemic intraphagocytic microbiota over time, and also to how much of the innate immune system is occupied keeping the 'nasties' at bay in the GI tract. The interesting thing is that although the MP abx profoundly change the gut flora, they do not wipe it out - as can be seen when discontinuing abx, the flora repopulates fairly quickly. I did once hear a presentation where it was claimed that a course of Cipro wiped out gut flora for a year. I don't believe that for a moment - the L-formsDifficult-to-culture bacteria that lack a cell wall and are not detectable by traditional culturing processes. Sometimes referred to as cell wall deficient bacteria. (like Hp) are clever little beasties… ..Trevor..

EXTREME PLEOMORPHISM AND THE BACTERIAL LIFE CYCLE: A FORGOTTEN CONTROVERSY

Science. 2009 Dec 18;326(5960):1694-7. Epub 2009 Nov 5. Bacterial community variation in human body habitats across space and time. Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R. Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA. Abstract Elucidating the biogeography of bacterial communities on the human body is critical for establishing healthy baselines from which to detect differences associated with diseases. To obtain an integrated view of the spatial and temporal distribution of the human microbiota, we surveyed bacteria from up to 27 sites in seven to nine healthy adults on four occasions. We found that community composition was determined primarily by body habitat. Within habitats, interpersonal variability was high, whereas individuals exhibited minimal temporal variability. Several skin locations harbored more diverse communities than the gut and mouth, and skin locations differed in their community assembly patterns. These results indicate that our microbiota, although personalized, varies systematically across body habitats and time; such trends may ultimately reveal how microbiome changes cause or prevent disease. PMID: 19892944

From genomics to proteomics. Tyers M, Mann M. Samuel Lunenfeld Research Institute, Mount Sinai Hospital, and Department of Medical Genetics and Microbiology, University of Toronto, Toronto, Canada M5G 1×5. tyers@mshri.on.ca Abstract Proteomics is the study of the function of all expressed proteins. Tremendous progress has been made in the past few years in generating large-scale data sets for protein-protein interactions, organelle composition, protein activity patterns and protein profiles in cancer patients. But further technological improvements, organization of international proteomics projects and open access to results are needed for proteomics to fulfil its potential. 71) A total of 14,000 physical interactions obtained from the GRID database were represented with the Osprey network visualization system (see http://biodata.mshri.on.ca/grid). Each edge in the graph represents an interaction between nodes, which are coloured according to Gene Ontology (GO) functional annotation. Highly connected complexes within the data set, shown at the perimeter of the central mass, are built from nodes that share at least three interactions within other complex members. The complete graph contains 4,543 nodes of 6,000 proteins encoded by the yeast genome, 12,843 interactions and an average connectivity of 2.82 per node. The 20 highly connected complexes contain 340 genes, 1,835 connections and an average connectivity of 5.39.

We still don't understand what a very large proportion of our DNA actually does. Sure, we understand how the genes work, but genes make up far less than half the total size of a the human genome. The non-gene, 'non-coding', regions are loosely termed “Junk DNA.” Well, a group at Oxford has started to hone in on one likely function: to perpetuate components of the Human Microbiome. Here is a simplified version of their hypothesis: http://www.tgdaily.com/general-sciences-features/52610-all-viruses-may-be-stowaways-within-our-dna And the more complex concepts are in two papers at PLOS. First, a commentary: http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001210 and then the actual paper: http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001191 This is an important concept, which I have touched upon a few times, but generally felt it too complex to explain in detail. Now this paper, and the two commentaries above, can help me communicate the concept ..Trevor.. http://blogs.nature.com/news/thegreatbeyond/2010/11/viruses_tk.html http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001191 It’s time for animals - including humans - to admit that the bacteria, viruses and other microbes have won. Our bodies are home to many times more bacterial cells than animal cells and countless trillions of viruses. Ancient retroviruses make up a good size chunk of our genome. Now, scientists have discovered that most any virus can set up shop in an animal's genomes and lay dormant for millions of years.

Mucosal Immunology (2011) 4, 133–138; doi:10.1038/mi.2010.89; published online 19 January 2011 A complex relationship: the interaction among symbiotic microbes, invading pathogens, and their mammalian host M M Curtis1 and V Sperandio1 1Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA Correspondence: V Sperandio, (Vanessa.Sperandio@utsouthwestern.edu) Received 1 October 2010; Accepted 13 December 2010; Published online 19 January 2011. Topof page Abstract Symbiosis between microbes and their mammalian host is vital to maintaining homeostasis. Symbiotic microbes within the gastrointestinal tract provide an array of benefits to the host, including promotion of host immunity. A coordinated effort of the host and symbiotic microbes deters the colonization and survival of many invading pathogens. However, pathogens have devised strategies to overcome these mechanisms. Furthermore, some pathogens can hijack host hormones and bacterial autoinducers to induce virulence traits. Intra- and inter-species (bacteria/bacteria) and interkingdom (bacteria/host) communication orchestrates the complex relationship among symbiotic microbes, invading pathogens, and their mammalian host. Insight into this communication will provide a foundation for the development of targeted antimicrobial therapies.

http://dx.doi.org/10.1371/journal.pbio.1001033 http://www.sciencedaily.com/releases/2011/03/110322172215.htm Most bacteria harbor toxin–antitoxin (TA) systems, in which a bacterial toxin is rendered inactive under resting conditions by its antitoxin counterpart. Under conditions of stress, however, the antitoxin is degraded, freeing the toxin to attack its host bacterium. One such TA system, PezAT, has been difficult to study in the past because the PezT toxin is so toxic without its antitoxin counterpart that bacteria die before any useful measurements can be made. Here, we use a truncated version of PezT that kills bacteria more slowly than normal, allowing us to examine the mechanisms of how this TA system operates. We find that zeta toxins convert an essential building block of bacterial cell walls (known as UNAG) into a form that prevents normal cell wall growth, causing distortions in bacterial shape that leave the bacteria vulnerable to the hydrostatic pressure of its contents. Consequently, the bacteria burst, similar to what happens when they are treated with penicillin. These results may serve useful for designing new antibiotics. Additionally, our results support the hypothesis that activation of PezT during bacterial infections may be a method by which rapidly growing bacteria can instigate a suicide program, which would promote the release of virulence factors that facilitate spread of infections.

Differential Attraction of Malaria Mosquitoes to Volatile Blends Produced by Human Skin Bacteria

Were we but able to explain

The fiefdom of the microbe—

Why one man is his serf,

Another is his lord

When all are his domain…. C.B.H, Mandell: Mandell, Douglas, and Bennett's Principles and Practice of Infectious Diseases

Viruses that Infect Parasites that Infect Us: The Matryoshka Dolls of Human Pathogens submitted by Chris Condayan on July 11, 2011 Tags: parasites, STC, viruses Source: schaechter.asmblog.org “We’re all too familiar with the viruses that can infect us, from the common cold to yellow fever virus to the endogenous retroviruses that make up a chunk of our genome. Many of us are also acquainted with parasites, such as tape worms or Giardia, that like to set up camp in the human body. But the world of parasites and viruses does not end there. Many parasites or endosymbionts can be infected with viruses. A classic example is Paramecium, which can harbor an endosymbiotic bacterium, Caedibacter, which in turn carries phages involved in making a toxin. But from the human point of view, things start to get particularly interesting when we consider the viruses that infect parasites of humans and how those viral infections—inside of a parasite inside of a person, somewhat like a Matryoshka nesting doll—may modulate the parasite’s interaction with its human host.”

BROKEN LINKS

?? * Microorganisms that inhabit our bodies could trigger some diseases - According to Dr. Marc Ouellette, scientific director of Canadian Institutes of Health Research's Institute of Infection and Immunity, “We're starting to realize that there are many, many possibilities or linkages between our microbiome and disease that we would not have expected before, especially complex diseases. This is really an emerging field where we think there are a lot of new discoveries to make that will have a direct impact in health.”