Antisense RNA that affects Rhodopseudomonas palustris quorum-sensingsignal receptor expression

Quorum sensing in the bacterium Rhodopseudomonas palustris involves the RpaI signal synthase, which produces p-coumaroyl-homoserine lactone (pC-HSL) and RpaR, which is a pC-HSL–dependent transcriptional activator. There is also an antisense rpaR transcript (asrpaR) of unknown function. Recent RNAseq studies have revealed that bacterial antisense RNAs are abundant, but little is known about the function of these molecules.

Role of Specific Quorum-Sensing Signals in the Regulation of Exopolysaccharide II Production within Sinorhizobium meliloti Spreading Colonies

Quorum sensing (QS) in Sinorhizobium meliloti involves at least half a dozen different N-acyl homoserine lactone (AHL) signals. These signals are produced by SinI, the sole AHL synthase in S. meliloti Rm8530. The sinI gene is regulated by two LuxR-type transcriptional regulators, SinR and ExpR. Mutations in sinI, sinR and expR abolish the production of exopolysaccharide II (EPS II).

Direct sampling of cystic fibrosis lungs indicates that DNA-based analyses of upper-airway specimens can misrepresent lung microbiota

Recent work using culture-independent methods suggests that the lungs of cystic fibrosis (CF) patients harbor a vast array of bacteria not conventionally implicated in CF lung disease. However, sampling lung secretions in living subjects requires that expectorated specimens or collection devices pass through the oropharynx.

Factors associated with the diversification of the gut microbial communities within chimpanzees from Gombe National Park

The gastrointestinal tract harbors large and diverse populations of bacteria that vary among individuals and within individuals over time. Numerous internal and external factors can influence the contents of these microbial communities, including diet, geography, physiology, and the extent of contact among hosts. To investigate the contributions of such factors to the variation and changes in gut microbial communities, authors analyzed the distal gut microbiota of individual chimpanzees from two communities in Gombe National Park, Tanzania.

A Novel Virulence Strategy for Pseudomonas aeruginosa Mediated by an Autotransporter with Arginine-Specific Aminopeptidase Activity

The opportunistic human pathogen, Pseudomonas aeruginosa, is a major cause of infections in chronic wounds, burns and the lungs of cystic fibrosis patients. The P. aeruginosa genome encodes at least three proteins exhibiting the characteristic three domain structure of autotransporters, but much remains to be understood about the functions of these three proteins and their role in pathogenicity.

New Insights in Gut Microbiota Establishment in Healthy Breast FedNeonates

The establishment of a pioneer gut microbiota is increasingly recognized as a crucial stage in neonatal development influencing health throughout life. While current knowledge is mainly based on either culture or molecular analysis of feces, authors of this article have opted for a comprehensive approach complementing culture with state-of-the-art molecular methods.

AtlasT4SS: A curated database for type IV secretion systems

The type IV secretion system (T4SS) can be classified as a large family of macromolecule transporter systems, divided into three recognized sub-families, according to the well-known functions. The major sub-family is the conjugation system, which allows transfer of genetic material, such as a nucleoprotein, via cell contact among bacteria. Also, the conjugation system can transfer genetic material from bacteria to eukaryotic cells; such is the case with the T-DNA transfer of Agrobacterium tumefaciens to host plant cells. The system of effector protein transport constitutes the second sub-family, and the third one corresponds to the DNA uptake/release system. Genome analyses have revealed numerous T4SS in Bacteria and Archea. The purpose of this work was to organize, classify, and integrate the T4SS data into a single database, called AtlasT4SS - the first public database devoted exclusively to this prokaryotic secretion system. Description The AtlasT4SS is a manual curated database that describes a large number of proteins related to the type IV secretion system reported so far in Gram-negative and Gram-positive bacteria, as well as in Archaea. The database was created using the SGBD MySQL and the Catalyst Framework based in Perl programming language and Model-View-Controller (MVC) design pattern for Web. The current version holds a comprehensive collection of 1,617 T4SS proteins from 58 Bacteria (49 Gram-negative and 9 Gram-Positive), one Archaea and 11 plasmids. By applying the bi-directional best hit (BBH) relationship in pairwise genome comparison, it was possible to obtain a core set of 134 clusters of orthologous genes encoding T4SS proteins.

This database present one way of classifying ortholog groups of T4SSs in a hierarchical classification scheme with three levels. The first level comprises four classes that are based on the organization of genetic determinants, shared homologies, and evolutionary relationships: (i) F-T4SS, (ii) P-T4SS, (iii) I-T4SS, and (iv) GI-T4SS. The second level designates a specific well-known protein families otherwise an uncharacterized protein family. Finally, in the third level, each protein of an ortholog cluster is classified according to its involvement in a specific cellular process. AtlasT4SS database is open access and is available at http://www.t4ss.lncc.br.

Original Source:

Microbial Biodiversity of Cell Phones and Shoes

The results are in!

So, what lives on reporters’ cell phones and shoes, you ask? As, you can see from the graph at left, quite a lot! Each vertical bar is one shoe or cell phone, and each color represents a different species of bacteria. The larger the colored block, the more prevalent the species. The most predominant species include:

• Mycoplasma (beige) – one of the smallest cells (0.1 μm diameter), also characterized by its resistance to antibiotics and role in respiratory illnesses including pneumonia.
• Moraxellaceae (fuchsia) – this family includes the causative agent of pink eye in cattle and human respiratory tract antibiotic-resistant pathogens.
• Sphingomonadaceae (orange) – widespread family of bacteria which can be found in both marine and terrestrial habitats. Some species are able to rapidly degrade plastics in landfills.
• Streptophyta (purple) – a cyanobacterium, this microbe uses photosynthesis in a manner similar to plants.
• Flavobacteriaceae (pink) – a group associated with diseases in fish, such as rainbow trout fry syndrome and bacterial cold water disease

You can click here to download detailed taxonomy counts and high-resolution images of this visualization.

*Note: The above descriptions of bacterial groups serve to highlight interesting features of very broad and diverse lineages; finding Mycoplasma and Moraxellaceae in these samples does not indicate an outbreak of pneumonia and pink eye.

Interestingly, many of the bacteria from these samples were unidentifiable; the light blue and red sections at the bottom of each bar represent species which could only be classified as “Bacteria” (as opposed to Archean or Eukarya) or which could not be classified at all.

You may also have noticed the alternating trends in this figure – that if you numbered the bars from left to right, that the even-numbered bars are different from the odd-numbered bars. This is because the odd-numbered bars represent bacteria from shoe soles and the even-numbered bars represent bacteria from cell phones! When you can see these trends with the unaided eye, you know you are onto something. And indeed, interrogating thebeta diversity of these samples using principle coordinate analysis tools (at right) reveals that bacterial populations group according to the surface they were sampled from.

These groupings belie that fact that some species are more common to cell phones and others are more common to shoes – to such a degree that you can take a “mystery swab” and, by examining the bacteria it contains, determine if it was used on a cell phone or shoe. So, you might ask, how are these communities different? What bacteria live on a shoe but not on a cell phone? From this study, there appear to be 56 species which statistically favor one environment over the other. Oddly, only four of the 56 prefer the cell phone environment. They are:

• Mycoplasma – 52% of phone bacteria vs 20% of shoe bacteria (q-value = 1E-8)
• Streptococcaceae – 2.44% vs 0.94% (q-value = 0.016) – some subspecies are responsible for strep throat and meningitis.
• Fusobacteriaceae – 0.26% vs 0.07% (q-value = 0.027) – pathogenic bacterium of the throat.
• Neisseriaceae – 0.55% vs 0.11% (q-value = 0.040) – can cause  gonorrhea and meningitis.

The four most abundant species that favored growing on shoes were:

• Moraxellaceae – 6.8% of shoe bacteria vs 2.9% of phone bacteria (q-value = 8E-5) – as described above.
• Sphingomonadaceae – 6.1% vs 1.0% (q-value = 2E-9) – as described above.
• Unidentified Gammaproteobacteria – 2.7% vs 1.6% (q-value = 5E-4) – very diverse class of bacteria – includes E. coli, Vibrio, and Salmonella.
• Unidentified Actinomycetales – 2.8% vs 1.4% (q-value = 5E-3) – a group of gram-positive bacteria used in the production of drugs for treating cancer and infections.

In summary, the cell phone in your pocket and the shoes on your feet are home to a diverse collection of bacteria. What’s more, the bacteria on your cell phone look a lot like the bacteria on other people’s cell phones, and the bacteria on your shoes are similar to those on the shoes of those around you. However, the microbial communities on your cell phone are distinct from the ones on your shoes. And although many of the bacteria that call you home are closely related to disease-causing pathogens, these microbes are in fact defending you from their more dangerous cousins. So next time you see something sticky on the ground, instead of walking around it, go ahead and give them a treat ;-)

Major components of this analysis were conducted using QIIME, a free and open-source software package available from http://www.qiime.org/. Funding for this project was provided by the Alfred P. Sloan Foundation through the University of Chicago and Argonne National Laboratory. Questions about this study may be directed to Daniel Smith at ds@anl.gov or posted in the comment section below.

Original Source

Home Microbiome Study

Most of us are aware of the bacteria on the surfaces we come in contact with. The doorknob for the bathroom, coins and paper currency in our pockets, handrails in subway cars, computer keyboards and mice at the library… the list of built environments on which microbes thrive is nearly endless. In our preoccupation with concern for what might be transferred from these surfaces to our hands, we often completely forget that the microbes living on our hands are also being transferred to everything we touch. And as dirty as some surfaces are, they pale in comparison to you and I. Numerically speaking, human beings are 90% bacteria! Even washing our hands and gargling with mouthwash does not erase their presence from our bodies, which is fortunate, because these bacteria are essential for our health and well-being by helping us digest food and keeping away more dangerous microbes.

Each person’s collection of microorganisms is different. And in fact, the collection of bacteria on your right hand is different from the collection on your left hand, and the bacteria on your cheek are different from the ones on your chin. The compositions of these bacterial communities change very little day-to-day.

Now think about the light-switch in your bedroom. The one that only you touch, using the same hand, every day. Does it match the bacterial fingerprint for your hand? And if it does, did you put your bacterial community on the light switch… or, did the light switch’s bacterial community jump to your hand? And what about the other surfaces in your home that you interact with every day such as floors, doorknobs, and countertops?

I want to find the answers to these questions. To do so, my colleagues at Argonne National Laboratory and I are looking for volunteers who are about to move to a different house to join the Home Microbiome Study. They will be asked to collect samples every other day for six weeks to monitor how the microbiomes of themselves and their house change in response to one another. This data will provide valuable information on how stable our microbiomes are, and whether our microbiomes colonize our house… or our house’s microbiome colonizes us!

Persons interested in participating in this study are encouraged to contact Daniel Smith at HomeMicrobiome@anl.gov for more information.

Original Source: http://homemicrobiome.com

Home Microbiome Study from dansmith01

Yeast prions form infectious amyloid inclusion bodies in bacteria

Prions were first identified as infectious proteins associated with fatal brain diseases in mammals. However, fungal prions behave as epigenetic regulators that can alter a range of cellular processes. These proteins propagate as self-perpetuating amyloid aggregates being an example of structural inheritance. The best-characterized examples are the Sup35 and Ure2 yeast proteins, corresponding to [PSI+] and [URE3] phenotypes, respectively.

Trypanosoma cruzi Immune Response Modulation Decreases Microbiota in Rhodnius prolixus Gut and Is Crucial for Parasite Survival and Development

Trypanosoma cruzi in order to complete its development in the digestive tract of Rhodnius prolixus needs to overcome the immune reactions and microbiota trypanolytic activity of the gut. Authors demonstrate that in R. prolixus following infection with epimastigotes of Trypanosoma cruzi clone Dm28c and, in comparison with uninfected control insects, the midgut contained (i) fewer bacteria, (ii) higher parasite numbers, and (iii) reduced nitrite and nitrate production and increased phenoloxidase and antibacterial activities.

Infection of human THP-1 cells with dormant Mycobacterium tuberculosis

Dormant, non-replicating Mycobacterium tuberculosis H37Rv strain cultured in hypoxic conditions was used to infect THP-1 cells. CFUs counting, Kinyoun staining and electron microscopy showed that dormant bacilli infected THP-1 cells at a rate similar to replicating M. tuberculosis, but failed to grow during the first 6 days of infection.

Daily follow-up of bacterial communities in the human gut reveals stable composition and host-specific patterns of interaction

In the last decade, an extensive effort has been made to characterize the human intestinal microbiota by means of SSU rRNA gene sequence and metagenomic analysis. Relatively few studies have followed intestinal bacterial communities over time to assess their stability in the absence of perturbation. In this study authors have monitored the faecal bacteria of three healthy subjects during fifteen consecutive days.

Capsule Type of Streptococcus pneumoniae Determines Growth Phenotype

Streptococcus pneumoniae bacteria are responsible for serious human infections including meningitis, pneumonia and bacteraemia and are a common cause of otitis media (ear infection) in children. However, they most often reside harmlessly in the infant nasopharynx. An association has long been observed between the type of polysaccharide capsule surrounding the bacteria and harmless colonization versus invasive disease.

Increased honey bee diversity means fewer pathogens, more helpful bacteria, IU biologist finds

Another first, research also finds probiotic species used by humans flourishing in colonies.

A novel study of honey bee genetic diversity co-authored by an Indiana University biologist has for the first time found that greater diversity in worker bees leads to colonies with fewer pathogens and more abundant helpful bacteria like probiotic species.

Microbial fuel cell: How bacteria can generate electricity

Bacillus stratosphericus is a bacteria that can generate electricity using a special battery called microbial fuel cell (MFC)

Bacillus stratosphericus can generate twice as much electricity as other types of common bacteria and can be used in a microbial fuel cell (MFC) to convert river waste into power and clean water. Scientists from Newcastle University believe they could be harvested and used in the developing world to power appliances.

MyMicrobes wants to sequence your gut microbiome

MyMicrobes is a social network that is inviting people to have their gut bacteria sequenced for about €1,500. The idea is act as social network and DNA database, offering a place for people to talk about diet tips and gastrointestinal woes.

A natural substance in a Chilean avocado plant combats multi-resistant bacterial strains of Staphylococcus

Researchers from the University of Copenhagen have discovered a compound (kaempferol rhamnoside ) that targets a particular resistance mechanism in yellow staphylococci. The development of resistance in these specific bacteria is extremely rapid. Bacterial strains that do not respond to treatment have already been found in the USA and Greece.