bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of host traits and geography in shaping the gut microbiome of insectivorous bats
Authors: Dai Wentao , Leng Haixia , Li Jun , Li Aoqiang , Li Zhongle , Zhu Yue , Li Xiaolin , Jin Longru , Sun Keping , Feng Jiang 
Published: March 2024

ABSTRACT

The gut microbiome is a symbiotic microbial community associated with the host and plays multiple important roles in host physiology, nutrition, and health. A number of factors have been shown to influence the gut microbiome, among which diet is considered to be one of the most important; however, the relationship between diet composition and gut microbiota in wild mammals is still not well recognized. Herein, we characterized the gut microbiota of bats and examined the effects of diet, host taxa, body size, gender, elevation, and latitude on the gut microbiota. The cytochrome C oxidase subunit I (COI) gene and 16S rRNA gene amplicons were sequenced from the feces of eight insectivorous bat species in southern China, including
Miniopterus fuliginosus
,
Aselliscus stoliczkanus
,
Myotis laniger
,
Rhinolophus episcopus
,
Rhinolophus osgoodi
,
Rhinolophus ferrumequinum
,
Rhinolophus affinis,
and
Rhinolophus pusillus
. The results showed that the composition of gut microbiome and diet exhibited significant differences among bat species. Diet composition and gut microbiota were significantly correlated at the order, family, genus, and operational taxonomic unit levels, while certain insects had a marked effect on the gut microbiome at specific taxonomic levels. In addition, elevation, latitude, body weight of bats, and host species had significant effects on the gut microbiome, but phylosymbiosis between host phylogeny and gut microbiome was lacking. These findings clarify the relationship between gut microbiome and diet and contribute to improving our understanding of host ecology and the evolution of the gut microbiome in wild mammals.

IMPORTANCE
The gut microbiome is critical for the adaptation of wildlife to the dynamic environment. Bats are the second-largest group of mammals with short intestinal tract, yet their gut microbiome is still poorly studied. Herein, we explored the relationships between gut microbiome and food composition, host taxa, body size, gender, elevation, and latitude. We found a significant association between diet composition and gut microbiome in insectivorous bats, with certain insect species having major impacts on gut microbiome. Factors like species taxa, body weight, elevation, and latitude also affected the gut microbiome, but we failed to detect phylosymbiosis between the host phylogeny and the gut microbiome. Overall, our study presents novel insights into how multiple factors shape the bat’s gut microbiome together and provides a study case on host-microbe interactions in wildlife.
Inoculation with
Stutzerimonas stutzeri
strains decreases N₂O emissions from vegetable soil by altering microbial community composition and diversity
Authors: Gao Nan , Zhang Huanhuan , Hu Chun , Li Qing , Li Linmei , Lei Peng , Xu Hong , Shen Weishou 
Published: March 2024

ABSTRACT

Inoculation with plant growth-promoting rhizobacteria (PGPR) strains has promoted plant growth and decreased nitrous oxide (N₂O) emissions from agricultural soils simultaneously. However, limited PGPR strains can mitigate N₂O emissions from agricultural soils, and the microbial ecological mechanisms underlying N₂O mitigation after inoculation are poorly understood. In greenhouse pot experiments, the effects of inoculation with
Stutzerimonas stutzeri
NRCB010 and NRCB025 on tomato growth and N₂O emissions were investigated in two vegetable agricultural soils with contrasting textures. Inoculation with NRCB010 and NRCB025 significantly promoted tomato growth in both soils. Moreover, inoculation with NRCB010 decreased the N₂O emissions from the fine- and coarse-textured soils by 38.7% and 52.2%, respectively, and inoculation with NRCB025 decreased the N₂O emissions from the coarse-textured soil by 76.6%. Inoculation with NRCB010 and NRCB025 decreased N₂O emissions mainly by altering soil microbial community composition and the abundance of nitrogen-cycle functional genes. The N₂O-mitigating effect might be partially explained by a decrease in the (
amoA + amoB
)/(
nosZ
I +
nosZ
II) and (
nirS + nirK
)/(
nosZ
I +
nosZ
II) ratios, respectively. Soil pH and organic matter were key variables that explain the variation in abundance of N-cycle functional genes and subsequent N₂O emission. Moreover, the N₂O-mitigating effect varied depending on soil textures and individual strain after inoculation. This study provides insights into developing biofertilizers with plant growth-promoting and N₂O-mitigating effects.

IMPORTANCE

Plant growth-promoting rhizobacteria (PGPR) have been applied to mitigate nitrous oxide (N₂O) emissions from agricultural soils, but the microbial ecological mechanisms underlying N₂O mitigation are poorly understood. That is why only limited PGPR strains can mitigate N₂O emissions from agricultural soils. Therefore, it is of substantial significance to reveal soil ecological mechanisms of PGPR strains to achieve efficient and reliable N₂O-mitigating effect after inoculation. Inoculation with
Stutzerimonas stutzeri
strains decreased N₂O emissions from two soils with contrasting textures probably by altering soil microbial community composition and gene abundance involved in nitrification and denitrification. Our findings provide detailed insight into soil ecological mechanisms of PGPR strains to mitigate N₂O emissions from vegetable agricultural soils.
First report of multidrug-resistant carbapenemase-producing
Aeromonas caviae
co-harboring
mcr-3.43
and
mcr-7.2
Authors: Xu Tingting , Song Jingjie , Liu Jialong , Huang Lili , Li Zhao , Zhou Kai 
Published: March 2024

ABSTRACT

Hospital sewage serves as a crucial reservoir for antibiotic resistance genes. As colistin and carbapenems are the last-resort antibiotics, the emergence of their resistance genes has become a significant concern in clinical settings. In this study, we found that two novel
mcr
alleles (
mcr-3
.43 and
mcr-7
.2) with two carbapenemase genes (
bla
NDM-1
and
bla
KPC-2
) were encoded in a single
Aeromonas caviae
strain isolated from hospital sewage. Our phylogenetic analysis revealed that the
mcr-3.43
gene clustered with
mcr-3.17
(with 95.55% amino acid identity), while the
mcr-7.2
gene clustered with
mcr-7.1
(with 68.68% amino acid identity). BLAST search against GenBank showed that
mcr-7.2
was exclusively detected in
Aeromonas
spp. Mobile genetic elements were not found in the genetic context of
mcr-7.2
, suggesting that the dissemination of
mcr-7.2
in
Aeromonas
spp. may be dependent on vertical transfer or recombination. The
bla
NDM-1
was adjacent to a recombinase gene and flanked by two IS
91
elements, indicating a potential mobilization mechanism mediated by recombination and/or ISs. The
bla
KPC-2
gene was located on an IncU plasmid and adjacent to an IS
Kpn6
. In summary, our study provides evidence for
Aeromonas
spp. as one of the potential reservoirs of colistin and carbapenem resistance genes.

IMPORTANCE

The study discovered two novel
mcr
genes (
mcr-3.43
and
mcr-7.2
) and two carbapenemase genes (
bla
NDM-1
and
bla
KPC-2
) in a single
Aeromonas caviae
strain retrieved from hospital sewage. Using phylogenetic analysis and comparative data evaluation, the study revealed the genetic relatedness and dissemination potential of the detected resistance genes. With the exclusive discovery that
mcr-7.2
is only present in
Aeromonas
spp. and the lack of mobile genetic elements in its genetic context, there is a strong indication of limited dissemination. The identification of these four resistance genes in a single strain of
Aeromonas
provided valuable insights into their potential presence in this genus. This study revealed that hospital sewage functions as a significant reservoir for antibiotic resistance genes, including colistin and carbapenem resistance genes.
Broad host range phages target global
Clostridium perfringens
bacterial strains and clear infection in five-strain model systems
Authors: Thanki Anisha M. , Osei Emmanuel K. , Whenham Natasha , Salter Michael G. , Bedford Mike R. , Masey O’Neill Helen V. , Clokie Martha R. J. 
Published: March 2024

ABSTRACT

Clostridium perfringens
is a prevalent bacterial pathogen in poultry, and due to the spread of antimicrobial resistance, alternative treatments are needed to prevent and treat infection. Bacteriophages (phages), viruses that kill bacteria, offer a viable option and can be used therapeutically to treat
C. perfringens
infections. The aim of this study was to isolate phages against
C. perfringens
strains currently circulating on farms across the world and establish their virulence and development potential using host range screening, virulence assays, and larva infection studies. We isolated 32 phages of which 19 lysed 80%–92% of our global
C. perfringens
poultry strain collection (
n
= 97). The virulence of these individual phages and 32 different phage combinations was quantified in liquid culture at multiple doses. We then developed a multi-strain
C. perfringens
larva infection model, to mimic an effective poultry model used by the industry. We tested the efficacy of 16/32 phage cocktails in the larva model. From this, we identified that our phage cocktail consisting of phages CPLM2, CPLM15, and CPLS41 was the most effective at reducing
C. perfringens
colonization in infected larvae when administered before bacterial challenge. These data suggest that phages do have significant potential to prevent and treat
C. perfringens
infection in poultry.

IMPORTANCE

Clostridium perfringens
causes foodborne illness worldwide, and 95% of human infections are linked to the consumption of contaminated meat, including chicken products. In poultry,
C. perfringens
infection causes necrotic enteritis, and associated mortality rates can be up to 50%. However, treating infections is difficult as the bacterium is becoming antibiotic-resistant. Furthermore, the poultry industry is striving toward reduced antibiotic usage. Bacteriophages (phages) offer a promising alternative, and to progress this approach, robust suitable phages and laboratory models that mimic
C. perfringens
infections in poultry are required. In our study, we isolated phages targeting
C. perfringens
and found that many lyse
C. perfringens
strains isolated from chickens worldwide. Consistent with other published studies, in the model systems we assayed here, when some phages were combined as cocktails, the infection was cleared most effectively compared to individual phage use.
Diverse winter communities and biogeochemical cycling potential in the under-ice microbial plankton of a subarctic river-to-sea continuum
Authors: Blais Marie-Amélie , Vincent Warwick F. , Vigneron Adrien , Labarre Aurélie , Matveev Alex , Coelho Lígia Fonseca , Lovejoy Connie 
Published: March 2024

ABSTRACT

Winter conditions greatly alter the limnological properties of lotic ecosystems and the availability of nutrients, carbon, and energy resources for microbial processes. However, the composition and metabolic capabilities of winter microbial communities are still largely uncharacterized. Here, we sampled the winter under-ice microbiome of the Great Whale River (Nunavik, Canada) and its discharge plume into Hudson Bay. We used a combination of 16S and 18S rRNA gene amplicon analysis and metagenomic sequencing to evaluate the size-fractionated composition and functional potential of the microbial plankton. These under-ice communities were diverse in taxonomic composition and metabolically versatile in terms of energy and carbon acquisition, including the capacity to carry out phototrophic processes and degrade aromatic organic matter. Limnological properties, community composition, and metabolic potential differed between shallow and deeper sites in the river, and between fresh and brackish water in the vertical profile of the plume. Community composition also varied by size fraction, with a greater richness of prokaryotes in the larger size fraction (>3 µm) and of microbial eukaryotes in the smaller size fraction (0.22–3 µm). The freshwater communities included cosmopolitan bacterial genera that were previously detected in the summer, indicating their persistence over time in a wide range of physico-chemical conditions. These observations imply that the microbial communities of subarctic rivers and their associated discharge plumes retain a broad taxonomic and functional diversity throughout the year and that microbial processing of complex terrestrial materials persists beneath the ice during the long winter season.

IMPORTANCE
Microbiomes vary over multiple timescales, with short- and long-term changes in the physico-chemical environment. However, there is a scarcity of data and understanding about the structure and functioning of aquatic ecosystems during winter relative to summer. This is especially the case for seasonally ice-covered rivers, limiting our understanding of these ecosystems that are common throughout the boreal, subpolar, and polar regions. Here, we examined the winter under-ice microbiome of a Canadian subarctic river and its entry to the sea to characterize the taxonomic and functional features of the microbial community. We found substantial diversity in both composition and functional capabilities, including the capacity to degrade complex terrestrial compounds, despite the constraints imposed by a prolonged seasonal ice-cover and near-freezing water temperatures. This study indicates the ecological complexity and importance of winter microbiomes in ice-covered rivers and the coastal marine environment that they discharge into.
Oman as a fragment of Ediacaran eastern Gondwana
Authors: Gómez-Pérez Irene , Morton Andrew , Rawahi Hussam Al , Frei Dirk 
Published: March 2024

Abstract
Comprehensive U-Pb detrital zircon geochronology of Ediacaran sandstones from Oman indicates that they originated from Neoproterozoic basement with a peak magmatic age of ca. 850–780 Ma (Tonian), with lesser Paleoproterozoic and Ediacaran sources and renewed magmatic input starting at ca. 550 Ma. Comparison with detrital zircons from the Arabian-Nubian and NW Indian Shields supports an eastern Gondwana affinity for the Ediacaran succession of Oman. Tonian basement sediment sources are present in Oman. Sources for older Paleoproterozoic zircons (ca. 2500 and 1800 Ma) are not found in Oman but are known from the cratonic Indian Shield. The signal of the main magmatic events of the juvenile Arabian-Nubian Shield, peaking at ca. 640–620 Ma, is rare or absent in the Ediacaran rock succession of Oman. However, deformed Ediacaran clastic units with an Arabian-Nubian Shield affinity occur in western Oman. Influx of latest Ediacaran–early Cambrian zircons (550–525 Ma) is interpreted as due to final Cambrian Angudan/Malagasy orogeny-related magmatism.
These results, together with new ages for volcano-sedimentary terranes in the subsurface of SW Oman and seismic observations, support the interpretation that the Ediacaran succession of Oman was deposited along the western, passive margin of the Greater Indian Shield, on the eastern (east and west in this paper refer to present-day coordinates) side of the Mozambique Ocean. Oman then collided with the Arabian-Nubian Shield in the early Cambrian, when the Angudan/Malagasy orogeny led to final consolidation of Gondwana. Our data support the inference that the youngest and final suture between the Indian and Arabian Shields lies in the subsurface of Oman along the early Cambrian western deformation front.
Disconformity-controlled hydrothermal dolomitization and cementation during basin evolution: Upper Triassic carbonates, UAE
Authors: Mansurbeg H. , Alsuwaidi M. , Morad D. , Morad S. , Tiepolo M. , Shahrokhi S. , Al-Aasm I.S. , Koyi H. 
Published: March 2024

Abstract
Petrography, fluid-inclusion microthermometry, stable isotope analyses, and radiometric (206Pb/238U) dating of Upper Triassic dolostones, saddle dolomite, and quartz and calcite cements were used to constrain the timing and conditions of dolomitization and cementation in the context of the tectonic evolution of a basin in the northern United Arab Emirates. Dolomitization (ca. 152.4 Ma) and precipitation of saddle dolomite (ca. 146.8 Ma), calcite (ca. 144.6 Ma), and quartz cements are attributed to focused synrifting flow of hot basinal brines into grain-supported limestones in which permeability was enhanced by incursion of meteoric waters beneath a disconformity surface. Another calcite cement generation (ca. 99.7 Ma) was formed by flow of hot brines during tectonic compression related to the obduction of Oman ophiolites in the Late Cretaceous. Thus, this paper provides new insights into (1) stratigraphic controls on and timing of hydrothermal (hot basinal brines) dolomitization, (2) the origin of closely associated intraformational limestones and dolostones, and (3) linkages between diagenesis and thermochemical modifications of basinal brines during tectonic evolution of sedimentary basins.
Income disparities in loss in life expectancy after colon and rectal cancers: a Swedish register-based study
Authors: Syriopoulou Elisavet , Osterman Erik , Miething Alexander , Nordenvall Caroline , Andersson Therese Marie-Louise 
Published: March 2024

BackgroundDifferences in the prognosis after colorectal cancer (CRC) by socioeconomic position (SEP) have been reported previously; however, most studies focused on survival differences at a particular time since diagnosis. We quantified the lifetime impact of CRC and its variation by SEP, using individualised income to conceptualise SEP.MethodsData included all adults with a first-time diagnosis of colon or rectal cancers in Sweden between 2008 and 2021. The analysis was done separately for colon and rectal cancers using flexible parametric models. For each cancer and income group, we estimated the life expectancy in the absence of cancer, the life expectancy in the presence of cancer and the loss in life expectancy (LLE).ResultsWe found large income disparities in life expectancy after a cancer diagnosis, with larger differences among the youngest patients. Higher income resulted in more years lost following a cancer diagnosis. For example, 40-year-old females with colon cancer lost 17.64 years if in the highest-income group and 13.68 years if in the lowest-income group. Rectal cancer resulted in higher LLE compared with colon cancer. Males lost a larger proportion of their lives. All patients, including the oldest, lost more than 30% of their remaining life expectancy. Based on the number of colon and rectal cancer diagnoses in 2021, colon cancer results in almost double the number of years lost compared with rectal cancer (24 669 and 12 105 years, respectively).ConclusionWhile our results should be interpreted in line with what individualised income represents, they highlight the need to address inequalities.
Inflammation biomarkers in the intracranial blood are associated with outcome in patients with ischemic stroke
Authors: Dargazanli Cyril , Blaquière Marine , Moynier Marinette , de Bock Frédéric , Labreuche Julien , ter Schiphorst Adrien , Derraz Imad , Radu Răzvan Alexandru , Gascou Gregory , Lefevre Pierre Henri , Rapido Francesca , Fendeleur Julien , Arquizan Caroline , Bourcier Romain , Marin Philippe , Machi Paolo , Cagnazzo Federico , Hirtz Christophe , Costalat Vincent , Marchi Nicola 
Published: March 2024

BackgroundPerforming endovascular treatment (EVT) in patients with acute ischemic stroke (AIS) allows a port of entry for intracranial biological sampling.ObjectiveTo test the hypothesis that specific immune players are molecular contributors to disease, outcome biomarkers, and potential targets for modifying AIS.MethodsWe examined 75 subjects presenting with large vessel occlusion of the anterior circulation and undergoing EVT. Intracranial blood samples were obtained by microcatheter aspiration, as positioned for stent deployment. Peripheral blood samples were collected from the femoral artery. Plasma samples were quality controlled by electrophoresis and analyzed using a Mesoscale multiplex for targeted inflammatory and vascular factors.ResultsWe measured 37 protein biomarkers in our sample cohort. Through multivariate analysis, adjusted for age, intravenous thrombolysis, pretreatment National Institutes of Health Stroke Scale and Alberta Stroke Program Early CT scores, we found that post-clot blood levels of interleukin-6 (IL-6) were significantly correlated (adjusted P value <0.05) with disability assessed by the modified Rankin Scale (mRS) score at 90 days, with medium effect size. Chemokine (C-C) ligand 17 CCL17/TARC levels were inversely correlated with the mRS score. Examination of peripheral blood showed that these correlations did not reach statistical significance after correction. Intracranial biomarker IL-6 level was specifically associated with a lower likelihood of favorable outcome, defined as a mRS score of 0–2.ConclusionsOur findings show a signature of blood inflammatory factors at the cerebrovascular occlusion site. The correlations between these acute-stage biomarkers and mRS score outcome support an avenue for add-on and localized immune modulatory strategies in AIS.
Identification of suspicious behavior through anomalies in the tracking data of fishing vessels
Authors: Rodríguez Jorge P. , Irigoien Xabier , Duarte Carlos M. , Eguíluz Víctor M. 
Published: March 2024

AbstractAutomated positioning devices can generate large datasets with information on the movement of humans, animals and objects, revealing patterns of movement, hot spots and overlaps among others. However, in the case of Automated Information Systems (AIS), attached to vessels, observed strange behaviors in the tracking datasets may come from intentional manipulation of the electronic devices. Thus, the analysis of anomalies can provide valuable information on suspicious behavior. Here, we analyze anomalies of fishing vessel trajectories obtained with the Automatic Identification System. The map of silent anomalies, those that occur when positioning data are absent for more than 24 hours, shows that they are most likely to occur closer to land, with 87.1% of anomalies observed within 100 km of the coast. This behavior suggests the potential of identifying silence anomalies as a proxy for illegal activities. With the increasing availability of high-resolution positioning of vessels and the development of powerful statistical analytical tools, we provide hints on the automatic detection of illegal activities that may help optimize the management of fishing resources.
Personalized Cadence Awareness for Next Basket Recommendation
Authors: Katz Ori , Barkan Oren , Koenigstein Noam 
Published: March 2024

This empirical study addresses the problem of Next Basket Repurchase Recommendation (NBRR), an often overlooked aspect of Next Basket Recommendation (NBR). While NBR aims to suggest items for a user’s next basket based on their prior basket history, NBRR focuses solely on recommending items previously purchased by the user. Despite the common ground between NBR and NBRR, the latter requires a distinct approach.
In this paper, we survey recent developments in the fields of NBR and NBRR, emphasizing the different strategies employed for these closely related challenges. In addition, we review the common characteristics of users’ repurchase patterns, which characterize the NBRR problem. Building on these insights, we introduce a novel hyper-convolutional model tailored to capture behavioral patterns associated with repeated purchases. To evaluate its effectiveness, we conduct experiments on three publicly available datasets, offering a comprehensive analysis across three levels of granularity: user-level, order-level, and item-level.
Our analysis illuminates the conditions under which the model excels and identifies scenarios where it may encounter challenges. This research contributes valuable insights into enhancing repurchase recommendation systems and advancing the understanding of user purchase behavior in general.