bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring a Possible Link between the Intestinal Microbiota and Feed Efficiency in Pigs
Authors: McCormack Ursula M. , Curião Tânia , Buzoianu Stefan G. , Prieto Maria L. , Ryan Tomas , Varley Patrick , Crispie Fiona , Magowan Elizabeth , Metzler-Zebeli Barbara U. , Berry Donagh , O'Sullivan Orla , Cotter Paul D. , Gardiner Gillian E. , Lawlor Peadar G. 
Published: May 2017

ABSTRACT

Feed efficiency (FE) is critical in pig production for both economic and environmental reasons. As the intestinal microbiota plays an important role in energy harvest, it is likely to influence FE. Therefore, our aim was to characterize the intestinal microbiota of pigs ranked as low, medium, and high residual feed intake ([RFI] a metric for FE), where genetic, nutritional, and management effects were minimized, to explore a possible link between the intestinal microbiota and FE. Eighty-one pigs were ranked according to RFI between weaning and day 126 postweaning, and 32 were selected as the extremes in RFI (12 low, 10 medium, and 10 high). Intestinal microbiota diversity, composition, and predicted functionality were assessed by 16S rRNA gene sequencing. Although no differences in microbial diversity were found, some RFI-associated compositional differences were revealed, principally among members of
Firmicutes
, predominantly in feces at slaughter (albeit mainly for low-abundance taxa). In particular, microbes associated with a leaner and healthier host (e.g.,
Christensenellaceae
,
Oscillibacter
, and
Cellulosilyticum
) were enriched in low RFI (more feed-efficient) pigs. Differences were also observed in the ileum of low RFI pigs; most notably,
Nocardiaceae
(
Rhodococcus
) were less abundant. Predictive functional analysis suggested improved metabolic capabilities in these animals, especially within the ileal microbiota. Higher ileal isobutyric acid concentrations were also found in low RFI pigs. Overall, the differences observed within the intestinal microbiota of low RFI pigs compared with that of their high RFI counterparts, albeit relatively subtle, suggest a possible link between the intestinal microbiota and FE in pigs.

IMPORTANCE
This study is one of the first to show that differences in intestinal microbiota composition, albeit subtle, may partly explain improved feed efficiency (FE) in low residual feed intake (RFI) pigs. One of the main findings is that, although microbial diversity did not differ among animals of varying FE, specific intestinal microbes could potentially be linked with porcine FE. However, as the factors impacting FE are still not fully understood, intestinal microbiota composition may not be a major factor determining differences in FE. Nonetheless, this work has provided a potential set of microbial biomarkers for FE in pigs. Although culturability could be a limiting factor and intervention studies are required, these taxa could potentially be targeted in the future to manipulate the intestinal microbiome so as to improve FE in pigs. If successful, this has the potential to reduce both production costs and the environmental impact of pig production.
Postepizootic Persistence of Asymptomatic Mycoplasma conjunctivae Infection in Iberian Ibex
Authors: Fernández-Aguilar Xavier , Cabezón Oscar , Granados José Enrique , Frey Joachim , Serrano Emmanuel , Velarde Roser , Cano-Manuel Francisco Javier , Mentaberre Gregorio , Ráez-Bravo Arián , Fandos Paulino , López-Olvera Jorge Ramón 
Published: May 2017

ABSTRACT

The susceptibility of the Iberian ibex (
Capra pyrenaica
) to
Mycoplasma conjunctivae
ocular infection and the changes in their interaction over time were studied in terms of clinical outcome, molecular detection, and IgG immune response in a captive population that underwent a severe infectious keratoconjunctivitis (IKC) outbreak.
Mycoplasma conjunctivae
was detected in the Iberian ibex, coinciding with the IKC outbreak. Its prevalence had a decreasing trend in 2013 that was consistent with the clinical resolution (August, 35.4%; September, 8.7%; November, 4.3%). Infections without clinical outcome were, however, still detected in the last handling in November. Sequencing and cluster analyses of the
M. conjunctivae
strains found 1 year later in the ibex population confirmed the persistence of the same strain lineage that caused the IKC outbreak but with a high prevalence (75.3%) of mostly asymptomatic infections and with lower DNA load of
M. conjunctivae
in the eyes (mean quantitative PCR [qPCR] cycle threshold [

C
T

], 36.1 versus 20.3 in severe IKC). Significant age-related differences of
M. conjunctivae
prevalence were observed only under IKC epizootic conditions. No substantial effect of systemic IgG on
M. conjunctivae
DNA in the eye was evidenced with a linear mixed-models selection, which indicated that systemic IgG does not necessarily drive the resolution of
M. conjunctivae
infection and does not explain the epidemiological changes observed. The results show how both epidemiological scenarios, i.e., severe IKC outbreak and mostly asymptomatic infections, can consecutively occur by entailing mycoplasma persistence.

IMPORTANCE
Mycoplasma
infections are reported in a wide range of epidemiological scenarios that involve severe disease to asymptomatic infections. This study allows a better understanding of the transition between two different
Mycoplasma conjunctivae
epidemiological scenarios described in wild host populations and highlights the ability of
M. conjunctivae
to adapt, persist, and establish diverse interactions with its hosts. The proportion of asymptomatic and clinical
M. conjunctivae
infections in a host population may not be regarded only in response to intrinsic host species traits (i.e., susceptibility) but also to a specific host-pathogen interaction, which in turn influences the infection dynamics. Both epidemic infectious keratoconjunctivitis and a high prevalence of asymptomatic
M. conjunctivae
infections may occur in the same host population, depending on the circulation of
M. conjunctivae
, its maintenance, and the progression of the host-pathogen interactions.
Impact of Acanthamoeba Cysts on Stress Resistance of Salmonella enterica Serovar Typhimurium, Yersinia enterocolitica 4/O:3, Listeria monocytogenes 1/2a, and Escherichia coli O:26
Authors: Lambrecht Ellen , Baré Julie , Sabbe Koen , Houf Kurt 
Published: May 2017

ABSTRACT

The formation of robust resting cysts enables
Acanthamoeba
to resist harsh environmental conditions. This study investigated to what extent these cysts are resistant to physical and chemical stresses as applied in food industry cleaning and disinfection procedures. Moreover, it was assessed whether certain intracystic meat-borne bacterial pathogens are more stress resistant than free-living bacterial monocultures and if intracystic passage and subsequent association with trophozoites induces cross-tolerance toward other stressors. Several physical and chemical stressors (NaCl, H
2
O
2
, benzalkonium chloride, 55°C, heating until boiling, ethanol, dishwashing detergent, and sodium hypochlorite) frequently used in domestic and industrial food-related environments were tested against (i)
Acanthamoeba castellanii
cysts, (ii) single strains of bacterial monocultures, (iii) intracystic bacteria, and (iv) bacteria after intracystic passage (cyst-primed bacteria). Only heating until boiling and hypochlorite treatment were cysticidal. After boiling, no viable trophozoites could be recovered from the cysts, and hypochlorite treatment caused a 1.34- to 4.72-log
10
cells/ml reduction in cyst viability. All treatments were effective in reducing or even eliminating the tested bacterial monocultures, whereas bacteria residing inside cysts were more tolerant toward these stressors. All cyst-primed bacteria exhibited an increased tolerance toward subsequent H
2
O
2
(>92% decrease in median log
10
CFU/ml reduction) and 70% ethanol (>99% decrease) treatments. Moreover, intracystic passage significantly increased the survival of
Yersinia enterocolitica
(74% decrease in median log
10
reduction),
Escherichia coli
(58%), and
Salmonella enterica
(48%) after NaCl treatment and of
E. coli
(96%),
S. enterica
(99%), and
Listeria monocytogenes
(99%) after sodium hypochlorite treatment compared with that of nonprimed bacteria.

IMPORTANCE
The results from this study demonstrated that both viable and nonviable amoebal cysts can protect internalized bacteria against stressful conditions. Moreover, cyst passage can induce cross-tolerance in bacteria, increasing their survival when exposed to selected stressors. These findings underscore the potential importance of free-living amoebae in food-related environments and their impact on the persistence of meat-borne bacterial pathogens.
Zinc Resistance within Swine-Associated Methicillin-Resistant Staphylococcus aureus Isolates in the United States Is Associated with Multilocus Sequence Type Lineage
Authors: Hau Samantha J. , Frana Timothy , Sun Jisun , Davies Peter R. , Nicholson Tracy L. 
Published: May 2017

ABSTRACT

Zinc resistance in livestock-associated methicillin-resistant
Staphylococcus aureus
(LA-MRSA) sequence type 398 (ST398) is primarily mediated by the
czrC
gene colocated with the
mecA
gene, encoding methicillin resistance, within the type V staphylococcal cassette chromosome
mec
(SCC
mec
) element. Because
czrC
and
mecA
are located within the same mobile genetic element, it has been suggested that the use of zinc in feed as an antidiarrheal agent has the potential to contribute to the emergence and spread of methicillin-resistant
S. aureus
(MRSA) in swine, through increased selection pressure to maintain the SCC
mec
element in isolates obtained from pigs. In this study, we report the prevalence of the
czrC
gene and phenotypic zinc resistance in U.S. swine-associated LA-MRSA ST5 isolates, MRSA ST5 isolates from humans with no swine contact, and U.S. swine-associated LA-MRSA ST398 isolates. We demonstrated that the prevalence of zinc resistance in U.S. swine-associated LA-MRSA ST5 isolates was significantly lower than the prevalence of zinc resistance in MRSA ST5 isolates from humans with no swine contact and swine-associated LA-MRSA ST398 isolates, as well as prevalences from previous reports describing zinc resistance in other LA-MRSA ST398 isolates. Collectively, our data suggest that selection pressure associated with zinc supplementation in feed is unlikely to have played a significant role in the emergence of LA-MRSA ST5 in the U.S. swine population. Additionally, our data indicate that zinc resistance is associated with the multilocus sequence type lineage, suggesting a potential link between the genetic lineage and the carriage of resistance determinants.

IMPORTANCE
Our data suggest that coselection thought to be associated with the use of zinc in feed as an antimicrobial agent is not playing a role in the emergence of livestock-associated methicillin-resistant
Staphylococcus aureus
(LA-MRSA) ST5 in the U.S. swine population. Additionally, our data indicate that zinc resistance is more associated with the multilocus sequence type lineage, suggesting a potential link between the genetic lineage and the carriage of resistance markers. This information is important for public health professionals, veterinarians, producers, and consumers.
Sulfide-Induced Dissimilatory Nitrate Reduction to Ammonium Supports Anaerobic Ammonium Oxidation (Anammox) in an Open-Water Unit Process Wetland
Authors: Jones Zackary L. , Jasper Justin T. , Sedlak David L. , Sharp Jonathan O. 
Published: May 2017

ABSTRACT

Open-water unit process wetlands host a benthic diatomaceous and bacterial assemblage capable of nitrate removal from treated municipal wastewater with unexpected contributions from anammox processes. In exploring mechanistic drivers of anammox, 16S rRNA gene sequencing profiles of the biomat revealed significant microbial community shifts along the flow path and with depth. Notably, there was an increasing abundance of sulfate reducers (
Desulfococcus
and other
Deltaproteobacteria
) and anammox microorganisms (
Brocadiaceae
) with depth. Pore water profiles demonstrated that nitrate and sulfate concentrations exhibited a commensurate decrease with biomat depth accompanied by the accumulation of ammonium. Quantitative PCR targeting the anammox hydrazine synthase gene,
hzsA
, revealed a 3-fold increase in abundance with biomat depth as well as a 2-fold increase in the sulfate reductase gene,
dsrA
. These microbial and geochemical trends were most pronounced in proximity to the influent region of the wetland where the biomat was thickest and influent nitrate concentrations were highest. While direct genetic queries for dissimilatory nitrate reduction to ammonium (DNRA) microorganisms proved unsuccessful, an increasing depth-dependent dominance of
Gammaproteobacteria
and diatoms that have previously been functionally linked to DNRA was observed. To further explore this potential, a series of microcosms containing field-derived biomat material confirmed the ability of the community to produce sulfide and reduce nitrate; however, significant ammonium production was observed only in the presence of hydrogen sulfide. Collectively, these results suggest that biogenic sulfide induces DNRA, which in turn can explain the requisite coproduction of ammonium and nitrite from nitrified effluent necessary to sustain the anammox community.

IMPORTANCE
This study aims to increase understanding of why and how anammox is occurring in an engineered wetland with limited exogenous contributions of ammonium and nitrite. In doing so, the study has implications for how geochemical parameters could potentially be leveraged to impact nutrient cycling and attenuation during the operation of treatment wetlands. The work also contributes to ongoing discussions about biogeochemical signatures surrounding anammox processes and enhances our understanding of the contributions of anammox processes in freshwater environments.
Environmental Spread of New Delhi Metallo-β-Lactamase-1-Producing Multidrug-Resistant Bacteria in Dhaka, Bangladesh
Authors: Islam Mohammad Aminul , Islam Moydul , Hasan Rashedul , Hossain M. Iqbal , Nabi Ashikun , Rahman Mahdia , Goessens Wil H. F. , Endtz Hubert P. , Boehm Alexandria B. , Faruque Shah M. 
Published: May 2017

ABSTRACT

Resistance to carbapenem antibiotics through the production of New Delhi metallo-β-lactamase-1 (NDM-1) constitutes an emerging challenge in the treatment of bacterial infections. To monitor the possible source of the spread of these organisms in Dhaka, Bangladesh, we conducted a comparative analysis of wastewater samples from hospital-adjacent areas (HAR) and from community areas (COM), as well as public tap water samples, for the occurrence and characteristics of NDM-1-producing bacteria. Of 72 HAR samples tested, 51 (71%) samples were positive for NDM-1-producing bacteria, as evidenced by phenotypic tests and the presence of the
bla
NDM-1
gene, compared to 5 of 41 (12.1%) samples from COM samples (
P
< 0.001). All tap water samples were negative for NDM-1-producing bacteria.
Klebsiella pneumoniae
(44%) was the predominant bacterial species among
bla
NDM-1
-positive isolates, followed by
Escherichia coli
(29%),
Acinetobacter
spp. (15%), and
Enterobacter
spp. (9%). These bacteria were also positive for one or more other antibiotic resistance genes, including
bla
CTX-M-1
(80%),
bla
CTX-M-15
(63%),
bla
TEM
(76%),
bla
SHV
(33%),
bla
CMY-2
(16%),
bla
OXA-48-like
(2%),
bla
OXA-1
(53%), and
bla
OXA-47-like
(60%) genes. Around 40% of the isolates contained a
qnr
gene, while 50% had 16S rRNA methylase genes. The majority of isolates hosted multiple plasmids, and plasmids of 30 to 50 MDa carrying
bla
NDM-1
were self-transmissible. Our results highlight a number of issues related to the characteristics and source of spread of multidrug-resistant bacteria as a potential public health threat. In view of the existing practice of discharging untreated liquid waste into the environment, hospitals in Dhaka city contribute to the potential dissemination of NDM-1-producing bacteria into the community.

IMPORTANCE
Infections caused by carbapenemase-producing
Enterobacteriaceae
are extremely difficult to manage due to their marked resistance to a wide range of antibiotics. NDM-1 is the most recently described carbapenemase, and the
bla
NDM-1
gene, which encodes NDM-1, is located on self-transmissible plasmids that also carry a considerable number of other antibiotic resistance genes. The present study shows a high prevalence of NDM-1-producing organisms in the wastewater samples from hospital-adjacent areas as a potential source for the spread of these organisms to community areas in Dhaka, Bangladesh. The study also examines the characteristics of the isolates and their potential to horizontally transmit the resistance determinants. The significance of our research is in identifying the mode of spread of multiple-antibiotic-resistant organisms, which will allow the development of containment measures, leading to broader impacts in reducing their spread to the community.
Genomic Analysis of Calderihabitans maritimus KKC1, a Thermophilic, Hydrogenogenic, Carboxydotrophic Bacterium Isolated from Marine Sediment
Authors: Omae Kimiho , Yoneda Yasuko , Fukuyama Yuto , Yoshida Takashi , Sako Yoshihiko 
Published: May 2017

ABSTRACT

Calderihabitans maritimus
KKC1 is a thermophilic, hydrogenogenic carboxydotroph isolated from a submerged marine caldera. Here, we describe the
de novo
sequencing and feature analysis of the
C. maritimus
KKC1 genome. Genome-based phylogenetic analysis confirmed that
C. maritimus
KKC1 was most closely related to the genus
Moorella
, which includes well-studied acetogenic members. Comparative genomic analysis revealed that, like
Moorella
,
C. maritimus
KKC1 retained both the CO
2
-reducing Wood-Ljungdahl pathway and energy-converting hydrogenase-based module activated by reduced ferredoxin, but it lacked the HydABC and NfnAB electron-bifurcating enzymes and pyruvate:ferredoxin oxidoreductase required for ferredoxin reduction for acetogenic growth. Furthermore,
C. maritimus
KKC1 harbored six genes encoding CooS, a catalytic subunit of the anaerobic CO dehydrogenase that can reduce ferredoxin via CO oxidation, whereas
Moorella
possessed only two CooS genes. Our analysis revealed that three
cooS
genes formed known gene clusters in other microorganisms, i.e.,
cooS
-acetyl coenzyme A (acetyl-CoA) synthase (which contained a frameshift mutation),
cooS
–energy-converting hydrogenase, and
cooF-cooS
-FAD-NAD oxidoreductase, while the other three had novel genomic contexts. Sequence composition analysis indicated that these
cooS
genes likely evolved from a common ancestor. Collectively, these data suggest that
C. maritimus
KKC1 may be highly dependent on CO as a low-potential electron donor to directly reduce ferredoxin and may be more suited to carboxydotrophic growth compared to the acetogenic growth observed in
Moorella
, which show adaptation at a thermodynamic limit.

IMPORTANCE
Calderihabitans maritimus
KKC1 and members of the genus
Moorella
are phylogenetically related but physiologically distinct. The former is a hydrogenogenic carboxydotroph that can grow on carbon monoxide (CO) with H
2
production, whereas the latter include acetogenic bacteria that grow on H
2
plus CO
2
with acetate production. Both species may require reduced ferredoxin as an actual “energy equivalent,” but ferredoxin is a low-potential electron carrier and requires a high-energy substrate as an electron donor for reduction. Comparative genomic analysis revealed that
C. maritimus
KKC1 lacked specific electron-bifurcating enzymes and possessed six CO dehydrogenases, unlike
Moorella
species. This suggests that
C. maritimus
KKC1 may be more dependent on CO, a strong electron donor that can directly reduce ferredoxin via CO dehydrogenase, and may exhibit a survival strategy different from that of acetogenic
Moorella
, which solves the energetic barrier associated with endergonic reduction of ferredoxin with hydrogen.
FFA2 activation combined with ulcerogenic COX inhibition induces duodenal mucosal injury via the 5-HT pathway in rats
Authors: Akiba Yasutada , Maruta Koji , Narimatsu Kazuyuki , Said Hyder , Kaji Izumi , Kuri Ayaka , Iwamoto Ken-ichi , Kuwahara Atsukazu , Kaunitz Jonathan D. 
Published: May 2017

Serotonin (5-HT), predominantly synthesized and released by enterochromaffin cells, is implicated in gastrointestinal symptoms such as emesis, abdominal pain, and diarrhea. Because luminal short-chain fatty acids (SCFAs) release 5-HT from enterochromaffin cells, which express the SCFA receptor free fatty acid receptor 2 (FFA2) in rat duodenum, we examined the effects of the selective FFA2 agonist phenylacetamide-1 (PA1) on duodenal 5-HT release with consequent bicarbonate secretion [duodenal bicarbonate secretion (DBS)] and on indomethacin (IND)-induced enteropathy. Intestinal injury was induced by IND (10 mg/kg sc) with or without PA1. We measured DBS in vivo in a duodenal loop perfused with PA1 while measuring 5-HT released in the portal vein. Duodenal blood flow was measured by laser-Doppler flowmetry. IND induced small intestinal ulcers with duodenal sparing. PA1 given with IND (IND + PA1) dose dependently induced duodenal erosions. IND + PA1-induced duodenal lesions were inhibited by the FFA2 antagonist GLPG-0974, ondansetron, or omeprazole but not by RS-23597 or atropine. Luminal perfusion of PA1 augmented DBS accompanied by increased portal blood 5-HT concentrations with approximately eight times more release at 0.1 mM than at 1 µM, with the effects inhibited by coperfusion of GLPG-0974. Luminal PA1 at 1 µM increased, but at 0.1 mM diminished, duodenal blood flow. Cosuperfusion of PA1 (0.1 mM) decreased acid-induced hyperemia, further reduced by IND pretreatment but restored by ondansetron. These results suggest that, although FFA2 activation enhances duodenal mucosal defenses, FFA2 overactivation during ulcerogenic cyclooxygenase inhibition may increase the vulnerability of the duodenal mucosa to gastric acid via excessive 5-HT release and 5-HT3receptor activation, implicated in foregut-related symptoms such as emesis and epigastralgia.NEW & NOTEWORTHY Luminal free fatty acid receptor 2 agonists stimulate enterochromaffin cells and release serotonin, which enhances mucosal defenses in rat duodenum. However, overdriving serotonin release with high luminal concentrations of free fatty acid 2 ligands such as short-chain fatty acids injures the mucosa by decreasing mucosal blood flow. These results are likely implicated in serotonin-related dyspeptic symptom generation because of small intestinal bacterial overgrowth, which is hypothesized to generate excess SCFAs in the foregut, overdriving serotonin release from enterochromaffin cells.