bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ultrastructure Variability of the Exosporium Layer of Clostridium difficile Spores from Sporulating Cultures and Biofilms
Authors: Pizarro-Guajardo Marjorie , Calderón-Romero Paulina , Paredes-Sabja Daniel 
Published: July 2016

ABSTRACT

The anaerobic sporeformer
Clostridium difficile
is the leading cause of nosocomial antibiotic-associated diarrhea in developed and developing countries. The metabolically dormant spore form is considered the morphotype responsible for transmission, infection, and persistence, and the outermost exosporium layer is likely to play a major role in spore-host interactions during recurrent infections, contributing to the persistence of the spore in the host. A recent study (M. Pizarro-Guajardo, P. Calderón-Romero, P. Castro-Córdova, P. Mora-Uribe, and D. Paredes-Sabja, Appl Environ Microbiol 82:2202–2209, 2016,
http://dx.doi.org/10.1128/AEM.03410-15
) demonstrated by transmission electron microscopy the presence of two ultrastructural morphotypes of the exosporium layer in spores formed from the same sporulating culture. However, whether these distinct morphotypes appeared due to purification techniques and whether they appeared during biofilm development remain unclear. In this communication, we demonstrate through transmission electron microscopy that these two exosporium morphotypes are formed under sporulation conditions and are also present in spores formed during biofilm development. In summary, this work provides definitive evidence that in a population of sporulating cells, spores with a thick outermost exosporium layer and spores with a thin outermost exosporium layer are formed.

IMPORTANCE
Clostridium difficile
spores are recognized as the morphotype of persistence and transmission of
C. difficile
infections. Spores of
C. difficile
are intrinsically resistant to all known antibiotic therapies. Development of spore-based removal strategies requires a detailed knowledge of the spore surface for proper antigen selection. In this context, in this work we provide definitive evidence that two types of spores, those with a thick outermost exosporium layer and those with a thin outermost exosporium layer, are formed in the same
C. difficile
sporulating culture or during biofilm development.
Transmission of Staphylococcus aureus from Humans to Green Monkeys in The Gambia as Revealed by Whole-Genome Sequencing
Authors: Senghore Madikay , Bayliss Sion C. , Kwambana-Adams Brenda A. , Foster-Nyarko Ebenezer , Manneh Jainaba , Dione Michel , Badji Henry , Ebruke Chinelo , Doughty Emma L. , Thorpe Harry A. , Jasinska Anna J. , Schmitt Christopher A. , Cramer Jennifer D. , Turner Trudy R. , Weinstock George , Freimer Nelson B. , Pallen Mark J. , Feil Edward J. , Antonio Martin 
Published: July 2016

ABSTRACT

Staphylococcus aureus
is an important pathogen of humans and animals. We genome sequenced 90
S. aureus
isolates from The Gambia: 46 isolates from invasive disease in humans, 13 human carriage isolates, and 31 monkey carriage isolates. We inferred multiple anthroponotic transmissions of
S. aureus
from humans to green monkeys (
Chlorocebus sabaeus
) in The Gambia over different time scales. We report a novel monkey-associated clade of
S. aureus
that emerged from a human-to-monkey switch estimated to have occurred 2,700 years ago. Adaptation of this lineage to the monkey host is accompanied by the loss of phage-carrying genes that are known to play an important role in human colonization. We also report recent anthroponotic transmission of the well-characterized human lineages sequence type 6 (ST6) and ST15 to monkeys, probably because of steadily increasing encroachment of humans into the monkeys' habitat. Although we have found no evidence of transmission of
S. aureus
from monkeys to humans, as the two species come into ever-closer contact, there might be an increased risk of additional interspecies exchanges of potential pathogens.

IMPORTANCE
The population structures of
Staphylococcus aureus
in humans and monkeys in sub-Saharan Africa have been previously described using multilocus sequence typing (MLST). However, these data lack the power to accurately infer details regarding the origin and maintenance of new adaptive lineages. Here, we describe the use of whole-genome sequencing to detect transmission of
S. aureus
between humans and nonhuman primates and to document the genetic changes accompanying host adaptation. We note that human-to-monkey switches tend to be more common than the reverse and that a novel monkey-associated clade is likely to have emerged from such a switch approximately 2,700 years ago. Moreover, analysis of the accessory genome provides important clues as to the genetic changes underpinning host adaptation and, in particular, shows that human-to-monkey switches tend to be associated with the loss of genes known to confer adaptation to the human host.
Variable High-Pressure-Processing Sensitivities for Genogroup II Human Noroviruses
Authors: Lou Fangfei , DiCaprio Erin , Li Xinhui , Dai Xianjun , Ma Yuanmei , Hughes John , Chen Haiqiang , Kingsley David H. , Li Jianrong 
Published: July 2016

ABSTRACT

Human norovirus (HuNoV) is a leading cause of foodborne diseases worldwide. High-pressure processing (HPP) is one of the most promising nonthermal technologies for the decontamination of viral pathogens in foods. However, the survival of HuNoVs after HPP is poorly understood because these viruses cannot be propagated
in vitro
. In this study, we estimated the survival of different HuNoV strains within genogroup II (GII) after HPP treatment using viral receptor-binding ability as an indicator. Four HuNoV strains (one GII genotype 1 [GII.1] strain, two GII.4 strains, and one GII.6 strain) were treated at high pressures ranging from 200 to 600 MPa. After treatment, the intact viral particles were captured by porcine gastric mucin-conjugated magnetic beads (PGM-MBs) that contained histo-blood group antigens, the functional receptors for HuNoVs. The genomic RNA copies of the captured HuNoVs were quantified by real-time reverse transcriptase PCR (RT-PCR). Two GII.4 HuNoVs had similar sensitivities to HPP. The resistance of HuNoV strains against HPP ranked as follows: GII.1 > GII.6 > GII.4, with GII.4 being the most sensitive. Evaluation of temperature and matrix effects on HPP-mediated inactivation of HuNoV GII.4, GII.1, and GII.6 strains showed that HuNoV was more easily inactivated at lower temperatures and at a neutral pH. In addition, phosphate-buffered saline (PBS) and minimal essential medium (MEM) can provide protective effects against HuNoV inactivation compared to H
2
O. Collectively, this study demonstrated that (i) different HuNoV strains within GII exhibited different sensitivities to high pressure, and (ii) HPP is capable of inactivating HuNoV GII strains by optimizing pressure parameters.

IMPORTANCE
Human norovirus (HuNoV) is a leading cause of foodborne disease worldwide. Noroviruses are highly diverse, both antigenically and genetically. Genogroup II (GII) contains the majority of HuNoVs, with GII genotype 4 (GII.4) being the most prevalent. Recently, GII.1 and GII.6 have emerged and caused many outbreaks worldwide. However, the survival of these GII HuNoVs is poorly understood because they are uncultivable
in vitro
. Using a novel receptor-binding assay conjugated with real-time RT-PCR, we found that GII HuNoVs had variable susceptibilities to high-pressure processing (HPP), which is one of the most promising food-processing technologies. The resistance of HuNoV strains to HPP ranked as follows: GII.1 > GII.6 > GII.4. This study highlights the ability of HPP to inactivate HuNoV and the need to optimize processing conditions based on HuNoV strain variability and sample matrix.
Comparative Profiling and Discovery of Novel Glycosylated Mycosporine-Like Amino Acids in Two Strains of the Cyanobacterium Scytonema cf. crispum
Authors: D'Agostino Paul M. , Javalkote Vivek S. , Mazmouz Rabia , Pickford Russell , Puranik Pravin R. , Neilan Brett A. 
Published: July 2016

ABSTRACT

The mycosporine-like amino acids (MAAs) are a group of small molecules with a diverse ecological distribution among microorganisms. MAAs have a range of physiological functions, including protection against UV radiation, making them important from a biotechnological perspective. In the present study, we identified a putative MAA (
mys
) gene cluster in two New Zealand isolates of
Scytonema
cf.
crispum
(UCFS10 and UCFS15). Homology to “
Anabaena
-type”
mys
clusters suggested that this cluster was likely to be involved in shinorine biosynthesis. Surprisingly, high-performance liquid chromatography analysis of
S
. cf.
crispum
cell extracts revealed a complex MAA profile, including shinorine, palythine-serine, and their hexose-bound variants. It was hypothesized that a short-chain dehydrogenase (UCFS15_00405) encoded by a gene adjacent to the
S
. cf.
crispum
mys
cluster was responsible for the conversion of shinorine to palythine-serine. Heterologous expression of MysABCE and UCFS15_00405 in
Escherichia coli
resulted in the exclusive production of the parent compound shinorine. Taken together, these results suggest that shinorine biosynthesis in
S
. cf.
crispum
proceeds via an
Anabaena
-type mechanism and that the genes responsible for the production of other MAA analogues, including palythine-serine and glycosylated analogues, may be located elsewhere in the genome.

IMPORTANCE
Recently, New Zealand isolates of
S
. cf.
crispum
were linked to the production of paralytic shellfish toxins for the first time, but no other natural products from this species have been reported. Thus, the species was screened for important natural product biosynthesis. The mycosporine-like amino acids (MAAs) are among the strongest absorbers of UV radiation produced in nature. The identification of novel MAAs is important from a biotechnology perspective, as these molecules are able to be utilized as sunscreens. This study has identified two novel MAAs that have provided several new avenues of future research related to MAA genetics and biosynthesis. Further, we have revealed that the genetic basis of MAA biosynthesis may not be clustered on the genome. The identification of the genes responsible for MAA biosynthesis is vital for future genetic engineering.
Escherichia coli O157:H7 Strain EDL933 Harbors Multiple Functional Prophage-Associated Genes Necessary for the Utilization of 5-
N
-Acetyl-9-
O
-Acetyl Neuraminic Acid as a Growth Substrate
Authors: Saile Nadja , Voigt Anja , Kessler Sarah , Stressler Timo , Klumpp Jochen , Fischer Lutz , Schmidt Herbert 
Published: July 2016

ABSTRACT

Enterohemorrhagic
Escherichia coli
(EHEC) O157:H7 strain EDL933 harbors multiple prophage-associated open reading frames (ORFs) in its genome which are highly homologous to the chromosomal
nanS
gene. The latter is part of the
nanCMS
operon, which is present in most
E. coli
strains and encodes an esterase which is responsible for the monodeacetylation of 5-
N
-acetyl-9-
O
-acetyl neuraminic acid (Neu5,9Ac
2
). Whereas one prophage-borne ORF (z1466) has been characterized in previous studies, the functions of the other
nanS
-homologous ORFs are unknown. In the current study, the
nanS
-homologous ORFs of EDL933 were initially studied
in silico
. Due to their homology to the chromosomal
nanS
gene and their location in prophage genomes, we designated them
nanS
-p and numbered the different
nanS
-p alleles consecutively from 1 to 10. The two alleles
nanS
-p2 and
nanS
-p4 were selected for production of recombinant proteins, their enzymatic activities were investigated, and differences in their temperature optima were found. Furthermore, a function of these enzymes in substrate utilization could be demonstrated using an
E. coli
C600Δ
nanS
mutant in a growth medium with Neu5,9Ac
2
as the carbon source and supplementation with the different recombinant NanS-p proteins. Moreover, generation of sequential deletions of all
nanS
-p alleles in strain EDL933 and subsequent growth experiments demonstrated a gene dose effect on the utilization of Neu5,9Ac
2
. Since Neu5,9Ac
2
is an important component of human and animal gut mucus and since the nutrient availability in the large intestine is limited, we hypothesize that the presence of multiple Neu5,9Ac
2
esterases provides them a nutrient supply under certain conditions in the large intestine, even if particular prophages are lost.

IMPORTANCE
In this study, a group of homologous prophage-borne
nanS
-p alleles and two of the corresponding enzymes of enterohemorrhagic
E. coli
(EHEC) O157:H7 strain EDL933 that may be important to provide alternative genes for substrate utilization were characterized.
Systematic Assessment of Nonproteolytic Clostridium botulinum Spores for Heat Resistance
Authors: Wachnicka Ewelina , Stringer Sandra C. , Barker Gary C. , Peck Michael W. 
Published: July 2016

ABSTRACT

Heat treatment is an important controlling factor that, in combination with other hurdles (e.g., pH, a
w
), is used to reduce numbers and prevent the growth of and associated neurotoxin formation by nonproteolytic
C. botulinum
in chilled foods. It is generally agreed that a heating process that reduces the spore concentration by a factor of 10
6
is an acceptable barrier in relation to this hazard. The purposes of the present study were to review the available data relating to heat resistance properties of nonproteolytic
C. botulinum
spores and to obtain an appropriate representation of parameter values suitable for use in quantitative microbial risk assessment. In total, 753
D
values and 436
z
values were extracted from the literature and reveal significant differences in spore heat resistance properties, particularly those corresponding to recovery in the presence or absence of lysozyme. A total of 503
D
and 338
z
values collected for heating temperatures at or below 83°C were used to obtain a probability distribution representing variability in spore heat resistance for strains recovered in media that did not contain lysozyme.

IMPORTANCE
In total, 753
D
values and 436
z
values extracted from literature sources reveal significant differences in spore heat resistance properties. On the basis of collected data, two
z
values have been identified,
z
= 7°C and
z
= 9°C, for spores recovered without and with lysozyme, respectively. The findings support the use of heat treatment at 90°C for 10 min to reduce the spore concentration by a factor of 10
6
, providing that lysozyme is not present during recovery. This study indicates that greater heat treatment is required for food products containing lysozyme, and this might require consideration of alternative recommendation/guidance. In addition, the data set has been used to test hypotheses regarding the dependence of spore heat resistance on the toxin type and strain, on the heating technique used, and on the method of
D
value determination used.
High-Level Culturability of Epiphytic Bacteria and Frequency of Biosurfactant Producers on Leaves
Authors: Burch Adrien Y. , Do Paulina T. , Sbodio Adrian , Suslow Trevor V. , Lindow Steven E. 
Published: July 2016

ABSTRACT

To better characterize the bacterial community members capable of biosurfactant production on leaves, we distinguished culturable biosurfactant-producing bacteria from nonproducers and used community sequencing to compare the composition of these distinct cultured populations with that from DNA directly recovered from leaves. Communities on spinach, romaine, and head lettuce leaves were compared with communities from adjacent samples of soil and irrigation source water. Soil communities were poorly described by culturing, with recovery of cultured representatives from only 21% of the prevalent operational taxonomic units (OTUs) (>0.2% reads) identified. The dominant biosurfactant producers cultured from soil included bacilli and pseudomonads. In contrast, the cultured communities from leaves are highly representative of the culture-independent communities, with over 85% of the prevalent OTUs recovered. The dominant taxa of surfactant producers from leaves were pseudomonads as well as members of the infrequently studied genus
Chryseobacterium
. The proportions of bacteria cultured from head lettuce and romaine leaves that produce biosurfactants were directly correlated with the culture-independent proportion of pseudomonads in a given sample, whereas spinach harbored a wider diversity of biosurfactant producers. A subset of the culturable bacteria in irrigation water also became enriched on romaine leaves that were irrigated overhead. Although our study was designed to identify surfactant producers on plants, we also provide evidence that most bacteria in some habitats, such as agronomic plant surfaces, are culturable, and these communities can be readily investigated and described by more classical culturing methods.

IMPORTANCE
The importance of biosurfactant production to the bacteria that live on waxy leaf surfaces as well as their ability to be accurately assessed using culture-based methodologies was determined by interrogating epiphytic populations by both culture-dependent and culture-independent methods. Biosurfactant production was much more frequently observed in cultured communities on leaves than in other nearby habitats, such as soil and water, suggesting that this trait is important to life on a leaf by altering either the leaf itself or the interaction of bacteria with water. While pseudomonads were the most common biosurfactant producers isolated, this habitat also selects for taxa, such as
Chryseobacterium
, for which this trait was previously unrecognized. The finding that most epiphytic bacterial taxa were culturable validates strategies using more classical culturing methodologies for their study in this habitat.
Niche-Specific Impact of a Symbiotic Function on the Persistence of Microbial Symbionts within a Natural Host
Authors: Verma Subhash C. , Miyashiro Tim 
Published: July 2016

ABSTRACT

How the function of microbial symbionts is affected by their population/consortium structure within a host remains poorly understood. The symbiosis established between
Euprymna scolopes
and
Vibrio fischeri
is a well-characterized host-microbe association in which the function and structure of
V. fischeri
populations within the host are known:
V. fischeri
populations produce bioluminescence from distinct crypt spaces within a dedicated host structure called the light organ. Previous studies have revealed that luminescence is required for
V. fischeri
populations to persist within the light organ and that deletion of the
lux
gene locus, which is responsible for luminescence in
V. fischeri
, leads to a persistence defect. In this study, we investigated the impact of bioluminescence on
V. fischeri
population structure within the light organ. We report that the persistence defect is specific to crypt I, which is the most developmentally mature crypt space within the nascent light organ. This result provides insight into the structure/function relationship that will be useful for future mechanistic studies of squid-
Vibrio
symbiosis. In addition, our report highlights the potential impact of the host developmental program on the spatiotemporal dynamics of host-microbe interactions.

IMPORTANCE
Metazoan development and physiology depend on microbes. The relationship between the symbiotic function of microbes and their spatial structure within the host environment remains poorly understood. Here we demonstrate, using a binary symbiosis, that the host requirement for the symbiotic function of the microbial symbiont is restricted to a specific host environment. Our results also suggest a link between microbial function and host development that may be a fundamental aspect of the more complex host-microbe interactions.
Effects of Glucose and Starch on Lactate Production by Newly Isolated Streptococcus bovis S1 from Saanen Goats
Authors: Chen Lianmin , Luo Yang , Wang Hongrong , Liu Shimin , Shen Yizhao , Wang Mengzhi 
Published: July 2016

ABSTRACT

When ruminants are fed high-concentrate diets,
Streptococcus bovis
proliferates rapidly and produces lactate, potentially causing rumen acidosis. Understanding the regulatory mechanisms of the metabolism of this species might help in developing dietary strategies to alleviate rumen acidosis.
S. bovis
strain S1 was newly isolated from the ruminal fluid of Saanen dairy goats and then used to examine the effects of glucose and starch on bacterial metabolism and gene regulation of the organic acid-producing pathway in cultures at a pH of 6.5. Glucose or starch was added to the culture medium at 1 g/liter, 3 g/liter (close to a normal range in the rumen fluid), or 9 g/liter (excessive level). Lactate was the dominant acid produced during the fermentation, and levels increased with the amount of glucose or starch in a dose-dependent manner (
P
< 0.001). The production of formate and acetate in the fermentation media fluctuated slightly with the dose but accounted for small fractions of the total acids. The activities of lactate dehydrogenase (LDH) and α-amylase (α-AMY) increased with the starch dose (
P
< 0.05), but the α-AMY activity did not change with the glucose dose. The relative expression levels of the genes
ldh
,
pfl
(encoding pyruvate formate lyase),
ccpA
(encoding catabolite control protein A), and α-
amy
were higher at a dose of 9 g/liter than at 1 g/liter (
P
< 0.05). Expression levels of
pfl
and α-
amy
genes were higher at 3 g/liter than at 1 g/liter (
P
< 0.05). The fructose 1,6-diphosphate (FDP) concentration tended to increase with the glucose and starch concentrations. In addition, the
S. bovis
S1 isolate fermented glucose much faster than starch. We conclude that the quantities of glucose and soluble starch had a major effect on lactate production due to the transcriptional regulation of metabolic genes.

IMPORTANCE
This work used a newly isolated
S. bovis
strain S1 from the rumen fluid of Saanen goats and examined the effects of glucose and soluble starch on organic acid patterns, enzyme activity, and expression of genes for
in vitro
fermentation. It was found that lactate was the dominant product from
S. bovis
strain S1, and the quantities of both glucose and starch in the medium were highly correlated with lactate production and with the corresponding changes in associated enzymes and genes. Therefore, manipulating the metabolic pathway of
S. bovis
to alter the dietary level of readily fermentable sugar and carbohydrates may be a strategy to alleviate rumen acidosis.