bluuebunny/crossref_metadata_2025_split huggingface dataset:
Helicobacter saguini, a Novel Helicobacter Isolated from Cotton-Top Tamarins with Ulcerative Colitis, Has Proinflammatory Properties and Induces Typhlocolitis and Dysplasia in Gnotobiotic IL-10
−/−
Mice
Authors: Shen Z. , Mannion A. , Whary M. T. , Muthupalani S. , Sheh A. , Feng Y. , Gong G. , Vandamme P. , Holcombe H. R. , Paster B. J. , Fox J. G. 
Published: June 2016

ABSTRACT

A urease-negative, fusiform, novel bacterium named
Helicobacter saguini
was isolated from the intestines and feces of cotton-top tamarins (CTTs) with chronic colitis.
Helicobacter
sp. was detected in 69% of feces or intestinal samples from 116 CTTs. The draft genome sequence, obtained by Illumina MiSeq sequencing, for
H. saguini
isolate MIT 97-6194-5, consisting of ∼2.9 Mb with a G+C content of 35% and 2,704 genes, was annotated using the NCBI Prokaryotic Genomes Automatic Annotation Pipeline.
H. saguini
contains homologous genes of known virulence factors found in other enterohepatic helicobacter species (EHS) and
H. pylori
. These include flagellin, γ-glutamyl transpeptidase (
ggt
), collagenase, the secreted serine protease
htrA
, and components of a type VI secretion system, but the genome does not harbor genes for cytolethal distending toxin (
cdt
).
H. saguini
MIT 97-6194-5 induced significant levels of interleukin-8 (IL-8) in HT-29 cell culture supernatants by 4 h, which increased through 24 h. mRNAs for the proinflammatory cytokines IL-1β, tumor necrosis factor alpha (TNF-α), IL-10, and IL-6 and the chemokine CXCL1 were upregulated in cocultured HT-29 cells at 4 h compared to levels in control cells. At 3 months postinfection, all
H. saguini
-monoassociated gnotobiotic C57BL/129 IL-10
−/−
mice were colonized and had seroconverted to
H. saguini
antigen with a significant Th1-associated increase in IgG2c (
P
< 0.0001).
H. saguini
induced a significant typhlocolitis, associated epithelial defects, mucosa-associated lymphoid tissue (MALT) hyperplasia, and dysplasia. Inflammatory cytokines IL-22, IL-17a, IL-1β, gamma interferon (IFN-γ), and TNF-α, as well as inducible nitric oxide synthase (iNOS) were significantly upregulated in the cecal tissues of infected mice. The expression of the DNA damage response molecule γ-H2AX was significantly higher in the ceca of
H. saguini
-infected gnotobiotic mice than in the controls. This model using a nonhuman primate
Helicobacter
sp. can be used to study the pathogenic potential of EHS isolated from primates with naturally occurring inflammatory bowel disease (IBD) and colon cancer.
Fecal Indole as a Biomarker of Susceptibility to Cryptosporidium Infection
Authors: Chappell Cynthia L. , Darkoh Charles , Shimmin Lawrence , Farhana Naveed , Kim Do-Kyun , Okhuysen Pablo C. , Hixson James 
Published: June 2016

ABSTRACT

Cryptosporidium
causes significant diarrhea worldwide, especially among children and immunocompromised individuals, and no effective drug treatment is currently available for those who need it most. In this report, previous volunteer infectivity studies have been extended to examine the association between fecal indole and indole-producing (IP) gut microbiota on the outcome of a
Cryptosporidium
infection. Fecal indole concentrations (FICs) of 50 subjects and 19 taxa of common gut microbiota, including six IP taxa (11 subjects) were determined in stool samples collected before and after a challenge with
Cryptosporidium
oocysts. At the baseline, the mean FIC (± the standard deviation) was 1.66 ± 0.80 mM in those who became infected after a challenge versus 3.20 ± 1.23 mM in those who remained uninfected (
P
= 0.0001). Only 11.1% of the subjects with a FIC of >2.5 mM became infected after a challenge versus 65.2% of the subjects with a FIC of <2.5 mM. In contrast, the FICs of infected subjects at the baseline or during diarrhea were not correlated with infection intensity or disease severity. The relative abundances (percent) of
Escherichia coli
,
Bacillus
spp., and
Clostridium
spp. were greater ≥2.5-fold in volunteers with a baseline FIC of >2.5 mM, while those of
Bacteroides
pyogenes
,
B. fragilis
, and
Akkermansia
muciniphila
were greater in those with a baseline FIC of <2.5 mM. These data indicate that some IP bacteria, or perhaps indole alone, can influence the ability of
Cryptosporidium
to establish an infection. Thus, preexisting indole levels in the gut join the oocyst dose and immune status as important factors that determine the outcome of
Cryptosporidium
exposure.
A Mutation in the 16S rRNA Decoding Region Attenuates the Virulence of Mycobacterium tuberculosis
Authors: Watanabe Shinya , Matsumura Kazunori , Iwai Hiroki , Funatogawa Keiji , Haishima Yuji , Fukui Chie , Okumura Kayo , Kato-Miyazawa Masako , Hashimoto Masahito , Teramoto Kanae , Kirikae Fumiko , Miyoshi-Akiyama Tohru , Kirikae Teruo 
Published: June 2016

ABSTRACT

Mycobacterium tuberculosis
contains a single rRNA operon that encodes targets for antituberculosis agents, including kanamycin. To date, only four mutations in the kanamycin binding sites of 16S rRNA have been reported in kanamycin-resistant clinical isolates. We hypothesized that another mutation(s) in the region may dramatically decrease
M. tuberculosis
viability and virulence. Here, we describe an rRNA mutation, U1406A, which was generated
in vitro
and confers resistance to kanamycin while highly attenuating
M. tuberculosis
virulence. The mutant showed decreased expression of 20% (
n
= 361) of mycobacterial proteins, including central metabolic enzymes, mycolic acid biosynthesis enzymes, and virulence factors such as antigen 85 complexes and ESAT-6. The mutation also induced three proteins, including KsgA (Rv1010; 16S rRNA adenine dimethyltransferase), which closely bind to the U1406A mutation site on the ribosome; these proteins were associated with ribosome maturation and translation initiation processes. The mutant showed an increase in 17S rRNA (precursor 16S rRNA) and a decrease in the ratio of 30S subunits to the 70S ribosomes, suggesting that the U1406A mutation in 16S rRNA attenuated
M. tuberculosis
virulence by affecting these processes.
Rotation of Vibrio fischeri Flagella Produces Outer Membrane Vesicles That Induce Host Development
Authors: Aschtgen Marie-Stephanie , Lynch Jonathan B. , Koch Eric , Schwartzman Julia , McFall-Ngai Margaret , Ruby Edward 
Published: June 2016

ABSTRACT

Using the squid-vibrio association, we aimed to characterize the mechanism through which
Vibrio fischeri
cells signal morphogenesis of the symbiotic light-emitting organ. The symbiont releases two cell envelope molecules, peptidoglycan (PG) and lipopolysaccharide (LPS) that, within 12 h of light organ colonization, act in synergy to trigger normal tissue development. Recent work has shown that outer membrane vesicles (OMVs) produced by
V. fischeri
are sufficient to induce PG-dependent morphogenesis; however, the mechanism(s) of OMV release by these bacteria has not been described. Like several genera of both beneficial and pathogenic bacteria,
V. fischeri
cells elaborate polar flagella that are enclosed by an extension of the outer membrane, whose function remains unclear. Here, we present evidence that along with the well-recognized phenomenon of blebbing from the cell's surface, rotation of this sheathed flagellum also results in the release of OMVs. In addition, we demonstrate that most of the development-inducing LPS is associated with these OMVs and that the presence of the outer membrane protein OmpU but not the LPS O antigen on these OMVs is important in triggering normal host development. These results also present insights into a possible new mechanism of LPS release by pathogens with sheathed flagella.

IMPORTANCE
Determining the function(s) of sheathed flagella in bacteria has been challenging, because no known mutation results only in the loss of this outer membrane-derived casing. Nevertheless, the presence of a sheathed flagellum in such host-associated genera as
Vibrio
,
Helicobacter
, and
Brucella
has led to several proposed functions, including physical protection of the flagella and masking of their immunogenic flagellins. Using the squid-vibrio light organ symbiosis, we demonstrate another role, that of
V. fischeri
cells require rotating flagella to induce apoptotic cell death within surface epithelium, which is a normal step in the organ's development. Further, we present evidence that this rotation releases apoptosis-triggering lipopolysaccharide in the form of outer membrane vesicles. Such release may also occur by pathogens but with different outcomes for the host.
The Bacterial
iprA
Gene Is Conserved across Enterobacteriaceae, Is Involved in Oxidative Stress Resistance, and Influences Gene Expression in Salmonella enterica Serovar Typhimurium
Authors: Herman Allison , Serfecz Jacquelyn , Kinnally Alexandra , Crosby Kathleen , Youngman Matthew , Wykoff Dennis , Wilson James W. 
Published: June 2016

ABSTRACT

The
iprA
gene (formerly known as
yaiV
or STM0374) is located in a two-gene operon in the
Salmonella enterica
serovar Typhimurium genome and is associated with altered expression during spaceflight and rotating-wall-vessel culture conditions that increase virulence. However,
iprA
is uncharacterized in the literature. In this report, we present the first targeted characterization of this gene, which revealed that
iprA
is highly conserved across
Enterobacteriaceae
. We found that
S
. Typhimurium,
Escherichia coli
, and
Enterobacter cloacae
Δ
iprA
mutant strains display a multi-log-fold increase in oxidative stress resistance that is complemented using a plasmid-borne wild-type (WT) copy of the
S
. Typhimurium
iprA
gene. This observation was also associated with increased catalase activity, increased
S
. Typhimurium survival in macrophages, and partial dependence on the
katE
gene and full dependence on the
rpoS
gene. Our results indicate that IprA protein activity is sensitive to deletion of the N- and C-terminal 10 amino acids, while a region that includes amino acids 56 to 80 is dispensable for activity. RNA sequencing (RNA-Seq) analysis revealed several genes altered in expression in the
S
. Typhimurium Δ
iprA
mutant strain compared to the WT, including those involved in fimbria formation,
spvABCD
-mediated virulence, ethanolamine utilization, the phosphotransferase system (PTS) transport, and flagellin phase switching from FlgB to FliC (likely a stochastic event) and several genes of hypothetical or putative function.

IMPORTANCE
Overall, this work reveals that the conserved
iprA
gene measurably influences bacterial biology and highlights the pool of currently uncharacterized genes that are conserved across bacterial genomes. These genes represent potentially useful targets for bacterial engineering, vaccine design, and other possible applications.
Interrogating Genes That Mediate Chlamydia trachomatis Survival in Cell Culture Using Conditional Mutants and Recombination
Authors: Brothwell Julie A. , Muramatsu Matthew K. , Toh Evelyn , Rockey Daniel D. , Putman Timothy E. , Barta Michael L. , Hefty P. Scott , Suchland Robert J. , Nelson David E. 
Published: June 2016

ABSTRACT

Intracellular bacterial pathogens in the family
Chlamydiaceae
are causes of human blindness, sexually transmitted disease, and pneumonia. Genetic dissection of the mechanisms of chlamydial pathogenicity has been hindered by multiple limitations, including the inability to inactivate genes that would prevent the production of elementary bodies. Many genes are also
Chlamydia
-specific genes, and chlamydial genomes have undergone extensive reductive evolution, so functions often cannot be inferred from homologs in other organisms. Conditional mutants have been used to study essential genes of many microorganisms, so we screened a library of 4,184 ethyl methanesulfonate-mutagenized
Chlamydia trachomatis
isolates for temperature-sensitive (TS) mutants that developed normally at physiological temperature (37°C) but not at nonphysiological temperatures. Heat-sensitive TS mutants were identified at a high frequency, while cold-sensitive mutants were less common. Twelve TS mutants were mapped using a novel markerless recombination approach, PCR, and genome sequencing. TS alleles of genes that play essential roles in other bacteria and chlamydia-specific open reading frames (ORFs) of unknown function were identified. Temperature-shift assays determined that phenotypes of the mutants manifested at distinct points in the developmental cycle. Genome sequencing of a larger population of TS mutants also revealed that the screen had not reached saturation. In summary, we describe the first approach for studying essential chlamydial genes and broadly applicable strategies for genetic mapping in
Chlamydia
spp. and mutants that both define checkpoints and provide insights into the biology of the chlamydial developmental cycle.

IMPORTANCE
Study of the pathogenesis of
Chlamydia
spp. has historically been hampered by a lack of genetic tools. Although there has been recent progress in chlamydial genetics, the existing approaches have limitations for the study of the genes that mediate growth of these organisms in cell culture. We used a genetic screen to identify conditional
Chlamydia
mutants and then mapped these alleles using a broadly applicable recombination strategy. Phenotypes of the mutants provide fundamental insights into unexplored areas of chlamydial pathogenesis and intracellular biology. Finally, the reagents and approaches we describe are powerful resources for the investigation of these organisms.
Multifaceted Interfaces of Bacterial Competition
Authors: Stubbendieck Reed M. , Straight Paul D. 
Published: June 2016

ABSTRACT
Microbial communities span many orders of magnitude, ranging in scale from hundreds of cells on a single particle of soil to billions of cells within the lumen of the gastrointestinal tract. Bacterial cells in all habitats are members of densely populated local environments that facilitate competition between neighboring cells. Accordingly, bacteria require dynamic systems to respond to the competitive challenges and the fluctuations in environmental circumstances that tax their fitness. The assemblage of bacteria into communities provides an environment where competitive mechanisms are developed into new strategies for survival. In this minireview, we highlight a number of mechanisms used by bacteria to compete between species. We focus on recent discoveries that illustrate the dynamic and multifaceted functions used in bacterial competition and discuss how specific mechanisms provide a foundation for understanding bacterial community development and function.
Functional Interaction between the Cytoplasmic ABC Protein LptB and the Inner Membrane LptC Protein, Components of the Lipopolysaccharide Transport Machinery in Escherichia coli
Authors: Martorana Alessandra M. , Benedet Mattia , Maccagni Elisa A. , Sperandeo Paola , Villa Riccardo , Dehò Gianni , Polissi Alessandra 
Published: June 2016

ABSTRACT

The assembly of lipopolysaccharide (LPS) in the outer leaflet of the outer membrane (OM) requires the transenvelope Lpt (lipopolysaccharide transport) complex, made in
Escherichia coli
of seven essential proteins located in the inner membrane (IM) (LptBCFG), periplasm (LptA), and OM (LptDE). At the IM, LptBFG constitute an unusual ATP binding cassette (ABC) transporter, composed by the transmembrane LptFG proteins and the cytoplasmic LptB ATPase, which is thought to extract LPS from the IM and to provide the energy for its export across the periplasm to the cell surface. LptC is a small IM bitopic protein that binds to LptBFG and recruits LptA via its N- and C-terminal regions, and its role in LPS export is not completely understood. Here, we show that the expression level of
lptB
is a critical factor for suppressing lethality of deletions in the C-terminal region of LptC and the functioning of a hybrid Lpt machinery that carries
Pa
-LptC, the highly divergent LptC orthologue from
Pseudomonas aeruginosa
. We found that LptB overexpression stabilizes C-terminally truncated LptC mutant proteins, thereby allowing the formation of a sufficient amount of stable IM complexes to support growth. Moreover, the LptB level seems also critical for the assembly of IM complexes carrying
Pa
-LptC which is otherwise defective in interactions with the
E. coli
LptFG components. Overall, our data suggest that LptB and LptC functionally interact and support a model whereby LptB plays a key role in the assembly of the Lpt machinery.

IMPORTANCE
The asymmetric outer membrane (OM) of Gram-negative bacteria contains in its outer leaflet an unusual glycolipid, the lipopolysaccharide (LPS). LPS largely contributes to the peculiar permeability barrier properties of the OM that prevent the entry of many antibiotics, thus making Gram-negative pathogens difficult to treat. In
Escherichia coli
the LPS transporter (the Lpt machine) is made of seven essential proteins (LptABCDEFG) that form a transenvelope complex. Here, we show that increased expression of the membrane-associated ABC protein LptB can suppress defects of LptC, which participates in the formation of the periplasmic bridge. This reveals functional interactions between these two components and supports a role of LptB in the assembly of the Lpt machine.
Transcriptome Remodeling Contributes to Epidemic Disease Caused by the Human Pathogen Streptococcus pyogenes
Authors: Beres Stephen B. , Kachroo Priyanka , Nasser Waleed , Olsen Randall J. , Zhu Luchang , Flores Anthony R. , de la Riva Ivan , Paez-Mayorga Jesus , Jimenez Francisco E. , Cantu Concepcion , Vuopio Jaana , Jalava Jari , Kristinsson Karl G. , Gottfredsson Magnus , Corander Jukka , Fittipaldi Nahuel , Di Luca Maria Chiara , Petrelli Dezemona , Vitali Luca A. , Raiford Annessa , Jenkins Leslie , Musser James M. 
Published: June 2016

ABSTRACT

For over a century, a fundamental objective in infection biology research has been to understand the molecular processes contributing to the origin and perpetuation of epidemics. Divergent hypotheses have emerged concerning the extent to which environmental events or pathogen evolution dominates in these processes. Remarkably few studies bear on this important issue. Based on population pathogenomic analysis of 1,200
Streptococcus pyogenes
type
emm
89 infection isolates, we report that a series of horizontal gene transfer events produced a new pathogenic genotype with increased ability to cause infection, leading to an epidemic wave of disease on at least two continents. In the aggregate, these and other genetic changes substantially remodeled the transcriptomes of the evolved progeny, causing extensive differential expression of virulence genes and altered pathogen-host interaction, including enhanced immune evasion. Our findings delineate the precise molecular genetic changes that occurred and enhance our understanding of the evolutionary processes that contribute to the emergence and persistence of epidemically successful pathogen clones. The data have significant implications for understanding bacterial epidemics and for translational research efforts to blunt their detrimental effects.

IMPORTANCE
The confluence of studies of molecular events underlying pathogen strain emergence, evolutionary genetic processes mediating altered virulence, and epidemics is in its infancy. Although understanding these events is necessary to develop new or improved strategies to protect health, surprisingly few studies have addressed this issue, in particular, at the comprehensive population genomic level. Herein we establish that substantial remodeling of the transcriptome of the human-specific pathogen
Streptococcus pyogenes
by horizontal gene flow and other evolutionary genetic changes is a central factor in precipitating and perpetuating epidemic disease. The data unambiguously show that the key outcome of these molecular events is evolution of a new, more virulent pathogenic genotype. Our findings provide new understanding of epidemic disease.
Effective Cytotoxic T Lymphocyte Targeting of Persistent HIV-1 during Antiretroviral Therapy Requires Priming of Naive CD8
+
T Cells
Authors: Smith Kellie N. , Mailliard Robbie B. , Piazza Paolo A. , Fischer Will , Korber Bette T. , Fecek Ronald J. , Ratner Deena , Gupta Phalguni , Mullins James I. , Rinaldo Charles R. 
Published: June 2016

ABSTRACT

Curing HIV-1 infection will require elimination of persistent cellular reservoirs that harbor latent virus in the face of combination antiretroviral therapy (cART). Proposed immunotherapeutic strategies to cure HIV-1 infection include enhancing lysis of these infected cells by cytotoxic T lymphocytes (CTL). A major challenge in this strategy is overcoming viral immune escape variants that have evaded host immune control. Here we report that naive CD8
+
T cells from chronic HIV-1-infected participants on long-term cART can be primed by dendritic cells (DC). These DC must be mature, produce high levels of interleukin 12p70 (IL-12p70), be responsive to CD40 ligand (CD40L), and be loaded with inactivated, autologous HIV-1. These DC-primed CD8
+
T cell responders produced high levels of gamma interferon (IFN-γ) in response to a broad range of both conserved and variable regions of Gag and effectively killed CD4
+
T cell targets that were either infected with the autologous latent reservoir-associated virus or loaded with autologous Gag peptides. In contrast, HIV-1-specific memory CD8
+
T cells stimulated with autologous HIV-1-loaded DC produced IFN-γ in response to a narrow range of conserved and variable Gag peptides compared to the primed T cells and most notably, displayed significantly lower cytolytic function. Our findings highlight the need to selectively induce new HIV-1-specific CTL from naive precursors while avoiding activation of existing, dysfunctional memory T cells in potential curative immunotherapeutic strategies for HIV-1 infection.

IMPORTANCE
Current immunotherapeutic approaches aim to enhance antiviral immunity against the HIV-1 reservoir; however, it has yet to be shown whether T cells from persons on cART can recognize and eliminate virus-infected cells. We show that in persons on cART a personalized medicine approach using their dendritic cells to stimulate their naive T cells induces potent effector CTL
in vitro
that recognize and eradicate HIV-1-infected CD4
+
T cells. Additionally, we show that the same stimulation of existing memory T cells results in cytokine secretion but limited effector function. Our study demonstrates that the naive T cell repertoire can recognize persistent HIV-1 during cART and supports immunotherapy strategies for an HIV-1 cure that targets naive T cells, rather than existing, dysfunctional, memory T cells.