bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diversified humoral immunity and impacts of booster vaccines: SARS-CoV-2 antibody profile and Omicron BA.2 neutralization before and after first or second boosters
Authors: Zhang Xiaochun Susan , Windau Anne , Meyers Jamie , Yang Xiaohua , Dong Feng 
Published: August 2024

ABSTRACT

This study aims to investigate humoral immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and assess the impact of booster vaccines. We recruited individuals scheduled to receive either the first (original formula) or the second (bivalent) booster following the initial two-dose SARS-CoV-2 vaccination. We tested for IgG antibodies targeting the spike protein receptor-binding domain (RBD), S1, S2, and nucleocapsid protein, as well as for neutralizing antibodies against Omicron BA.2, before and 14–28 days after receiving the boosters. One year after receiving the initial series of vaccinations, all participants maintained anti-RBD/S1 antibodies. However, levels were lower in individuals who were vaccinated only compared to those who had both vaccination and prior infection (hybrid immunity). Participants with hybrid immunity also showed higher retention of neutralizing antibodies (93% compared to 24% in vaccine-only individuals). Even before receiving any booster shots, participants with hybrid immunity had antibody levels similar to those of vaccine-only individuals after their first booster. After receiving booster shots, antibody levels at 14–28 days were similar regardless of the number of boosters or the type of immunity. About 1 year after the first booster, all participants maintained neutralizing antibodies, and vaccine-only individuals retained about 10 times higher levels of binding antibodies than those without a booster. Humoral immunity varies widely among individuals, and vaccination planning should consider both vaccination and infection history. Boosters are beneficial for increasing antibody levels to ensure sufficient protection against infection and helping bridge the immunity gap between vaccine-only and hybrid immunity.

IMPORTANCE
As we move into the era of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine boosters and shifting from pandemic to endemic, the landscape has changed for both the circulating SARS-CoV-2 variants and population immunity. Even though recent waves of infection have been clinically milder than earlier variants due to the high levels of population immunity and the properties of the Omicron subvariants, vaccination remains crucial for managing COVID-19 in the post-pandemic era. Our study unveils significant variations in the retention of anti-SARS-CoV-2 binding antibody profiles and neutralizing antibody levels 1 year after the primary and the first booster mRNA vaccination. It adds new information regarding how boosters change antibody levels and durability in individuals with hybrid (vaccination plus infection) or vaccine-only (never-infected) immunity. The findings can shed light on future vaccination planning.
Unveiling the multifaceted potential of
Pseudomonas khavaziana
strain SR9: a promising biocontrol agent for wheat crown rot
Authors: Guo Shengzhi , Liu Yuqi , Yin Yanling , Chen Yating , Jia Siyu , Wu Tong , Liao Jun , Jiang Xinyan , Kareem Hafiz Abdul , Li Xuejun , Pan Junfeng , Wang Yao , Shen Xihui 
Published: August 2024

ABSTRACT

Fusarium pseudograminearum
, a soil-borne fungus, is the cause of the devastating wheat disease known as wheat crown rot (WCR). The persistence of this pathogen in the soil and crop residues contributes to the increased occurrence and severity of WCR. Therefore, developing effective strategies to prevent and manage WCR is of great importance. In this study, we isolated a bacterial strain, designated as SR9, from the stem of wheat, that exhibited potent antagonistic effects against
F. pseudograminearum
, as well as the biocontrol efficacy of SR9 on WCR was quantified at 83.99% ± 0.11%. We identified SR9 as
Pseudomonas khavaziana
and demonstrated its potential as a plant probiotic. SR9 displayed broad-spectrum antagonism against other fungal pathogens, including
Neurospora dictyophora
,
Botrytis californica
, and
Botryosphaeria dothidea
. Whole-genome sequencing analysis revealed that SR9 harbored genes encoding various cell wall-degrading enzymes, cellulases, and lipases, along with antifungal metabolites, which are responsible for its antagonistic activity. Gene knockout and quantitative PCR analyses reveal that phenazine is the essential factor for antagonism. SR9 possessed genes related to auxin synthesis, flagellar biosynthesis, biofilm adhesion, and the chemotaxis system, which play pivotal roles in plant colonization and growth promotion; we also evaluated the effects of SR9 on plant growth in wheat and
Arabidopsis
. Our findings strongly suggest that SR9 holds great promise as a biocontrol agent for WCR in sustainable agriculture.

IMPORTANCE

The escalating prevalence of wheat crown rot, primarily attributed to
Fusarium pseudograminearum
, necessitates the development of cost-effective and eco-friendly biocontrol strategies. While plant endophytes are recognized for their biocontrol potential, reports on effective strains targeting wheat crown rot are sparse. This study introduces the
Pseudomonas khavaziana
SR9 strain as an efficacious antagonist to the wheat crown rot pathogen
Fusarium pseudograminearum
. Demonstrating a significant reduction in wheat crown rot incidence and notable plant growth promotion, SR9 emerges as a key contributor to plant health and agricultural sustainability. Our study outlines a biological approach to tackle wheat crown rot, establishing a groundwork for innovative sustainable agricultural practices.
Distinct biogeographic patterns for bacteria and fungi in association with
Bursaphelenchus xylophilus
nematodes and infested pinewood
Authors: Cao Yuyu , Yang Nan , Gu Jianfeng , Zhang Xingyao , Ye Jianren , Chen Jianping , Li Hongjie 
Published: August 2024

ABSTRACT

Pinewood nematodes (PWN,
Bursaphelenchus xylophilus
) are destructive plant parasitic nematodes that cause pine wilt disease (PWD) by attacking the vascular systems of pine trees, resulting in widespread tree mortality. Research has shown that there are connections between nematode-associated microbes and PWD. Yet the variations in microbial communities across different geographic regions are not well-understood. In this study, we examined the bacterial and fungal communities associated with nematodes and infested wood collected from 34 sites across three vegetation zones in China, as well as samples from the United States, using 16S rRNA and internal transcribed spacer (ITS) gene amplicon sequencing. The predominant genera
Pseudomonas
and
Rhodococcus
were found in nematodes, and
Acinetobacter
was present in the wood of PWD-infected pine trees across China. Network analysis revealed that core bacterial taxa belonged to the Pseudomonadota and Actinomycetota phyla for the nematodes, whereas the Pseudomonadota and Bacteroidota phyla were dominant in the infested wood. Identification of enriched key microbial taxa in nematodes and infested wood across vegetation zones indicates distinct biogeographic microbial community structures and key bacterial species. Although the nematode-associated bacterial community showed consistency across geographic distances, the similarity of the PWD pine trees’ bacterial community decreased with distance, suggesting a spatial correlation with environmental variables. Our findings enhance our understanding of the microbiota associated with pinewood nematode (PWN) and offer valuable insights into PWD management.

IMPORTANCE

Our research uncovered specific bacteria and fungi linked to pinewood nematode (PWN) and infested wood in three different vegetation zones in China, as well as samples from the United States. This sheds light on the critical roles of certain microbial groups, such as
Pseudomonas, Acinetobacter
, and
Stenotrophomonas
, in influencing PWN fitness. Understanding these patterns provides valuable insights into the dynamics of PWN-associated microbiomes, offering potential strategies for managing pine wilt disease (PWD). We found significant correlations between geographic distance and similarity in bacterial communities in the infested wood, indicating a spatial influence on wood-associated microbial communities due to limited dispersal and localized environmental conditions. Further investigations of these spatial patterns and driving forces are crucial for understanding the ecological processes that shape microbial communities in complex ecosystems and, ultimately, for mitigating the transmission of PWN in forests.
A comparison of wild boar and domestic pig microbiota does not reveal a loss of microbial species but an increase in alpha diversity and opportunistic genera in domestic pigs
Authors: Rahman Rajibur , Fouhse Janelle M. , Ju Tingting , Fan Yi , S. Marcolla Camila , Pieper Robert , Brook Ryan K. , Willing Benjamin P. 
Published: August 2024

ABSTRACT

The microbiome of wild animals is believed to be co-evolved with host species, which may play an important role in host physiology. It has been hypothesized that the rigorous hygienic practices in combination with antibiotics and diets with simplified formulas used in the modern swine industry may negatively affect the establishment and development of the gut microbiome. In this study, we evaluated the fecal microbiome of 90 domestic pigs sampled from nine farms in Canada and 39 wild pigs sampled from three different locations on two continents (North America and Europe) using 16S rRNA gene amplicon sequencing. Surprisingly, the gut microbiome in domestic pigs exhibited higher alpha-diversity indices than wild pigs (
P
< 0.0001). The wild pig microbiome showed a lower Firmicutes-to-Bacteroidetes ratio and a higher presence of bacterial phyla Elusimicrobiota, Verrucomicrobiota, Cyanobacteria, and Fibrobacterota when compared to their domestic counterparts. At the genus level, the wild pig microbiome had enriched genera that were known for fiber degradation and short-chain fatty acid production. Interestingly, the phylum Fusobacteriota was only observed in domestic pigs. We identified 31 ASVs that were commonly found in the pig gut microbiome, regardless of host sources, which could be recognized as members of the core gut microbiome. Interestingly, we found five ASVs missing in domestic pigs that were prevalent in wild ones, whereas domestic pigs harbored 59 ASVs that were completely absent in wild pigs. The present study sheds light on the impact of domestication on the pig gut microbiome, including the gain of new genera, which might provide the basis to identify novel targets to manipulate the pig gut microbiome for improved health.

IMPORTANCE
The microbiome of pigs plays a crucial role in shaping host physiology and health. This study sought to identify if domestication and current rearing practices have resulted in a loss of co-evolved bacterial species by comparing the microbiome of wild boar and conventionally raised pigs. It provides a comparison of domestic and wild pigs with the largest sample sizes and is the first to examine wild boars from multiple sites and continents. We were able to identify core microbiome members that were shared between wild and domestic populations, and on the contrary to expectation, few microbes were identified to be lost from wild boar. Nevertheless, the microbiome of wild boars had a lower abundance of important pathogenic genera and was distinct from domestic pigs. The differences in the microbial composition may identify an opportunity to shift the microbial community of domestic pigs towards that of wild boar with the intent to reduce pathogen load.
Mining metagenomic data to gain a new insight into the gut microbial biosynthetic potential in placental mammals
Authors: Hu Dini , Zhang Tongzuo , He Shunfu , Pu Tianchun , Yin Yanqiang , Hu Yibo 
Published: August 2024

ABSTRACT

Mammals host a remarkable diversity and abundance of gut microbes. Biosynthetic gene clusters (BGCs) in microbial genomes encode biologically active chemical products and play an important role in microbe–host interactions. Traditionally, the exploration of gut microbial metabolic functions has relied on the pure culture method. However, given the limited amounts of microbes being cultivated, insights into the metabolism of gut microbes in mammals continued to be very limited. In this study, we adopted a computational pipeline for mining the metagenomic data (named taxonomy-guided identification of biosynthetic gene clusters, TaxiBGC) to identify experimentally verified BGCs in 373 metagenomes across 53 mammalian species in an unbiased manner. We demonstrated that polyketides (PKs) and nonribosomal peptides (NRPs) are representative of mammals, and the products derived from them were associated with cell–cell communication and resistance to inflammation. Large carnivores had the highest number of BGCs, followed by large herbivores and small mammals. We also observed that the large mammals had more common BGCs that aid in the biosynthesis of a variety of natural products. However, small mammals not only had fewer BGCs but were also unique to each species. Our results provide novel insights into the mining of metagenomic data sets to identify active BGCs and their products across mammals.

IMPORTANCE
The gut microbes host numerous biosynthetic gene clusters (BGCs) that biosynthesize natural products and impact the host’s physiology. Historically, our understanding of BGCs in mammalian gut microbes was largely based on studies on cultured isolates; however, only a small fraction of mammal-associated microbes have been investigated. The biochemical diversity of the mammalian gut microbiota is poorly understood. Metagenomic sequencing contains data from a vast number of organisms and provides information on the total gene content of communities. Unfortunately, the existing BGC prediction tools are designed for individual microbial genomes. Recently, a BGC prediction tool called the taxonomy-guided identification of biosynthetic gene clusters (TaxiBGC) that directly mine the metagenome was developed. To gain new insights into the microbial metabolism, we used TaxiBGC to predict BGCs from 373 metagenomes across 53 mammalian species representing seven orders. Our findings elucidate the functional activities of complex microbial communities in the gut.
Plumbagin enhances antimicrobial and anti-biofilm capacities of chlorhexidine against clinical
Klebsiella pneumoniae
while reducing resistance mutations
Authors: Liu Haifeng , Chen Huanchang , Ma Zhexiao , Zhang Ying , Zhang Shihang , Zhao Deyi , Yao Zhuocheng , Zhou Tieli , Wang Zhongyong 
Published: August 2024

ABSTRACT

With the widespread misuse of disinfectants, the clinical susceptibility of
Klebsiella pneumoniae
(
K. pneumoniae
) to chlorhexidine (CHX) has gradually diminished, posing significant challenges to clinical disinfection and infection control.
K. pneumoniae
employs overexpression of efflux pumps and the formation of thick biofilms to evade the lethal effects of CHX. Plumbagin (PLU) is a natural plant extract that enhances membrane permeability and reduces proton motive force. In this study, we elucidated the synergistic antimicrobial activity of PLU in combination with CHX, effectively reducing the MIC of CHX against
K. pneumoniae
to 1 µg/mL and below. Crucially, through crystal violet staining and confocal laser scanning microscopy live/dead staining, we discovered that PLU significantly enhances the anti-biofilm capability of CHX. Mechanistically, experiments involving membrane permeability, alkaline phosphatase leakage, reactive oxygen species, and RT-qPCR suggest that the combination of PLU and CHX improves the permeability of bacterial inner and outer membranes, promotes bacterial oxidative stress, and inhibits oqxA/B efflux pump expression. Furthermore, we conducted surface disinfection experiments on medical instruments to simulate clinical environments, demonstrating that the combination effectively reduces bacterial loads by more than 3 log
10
CFU/mL. Additionally, results from resistance mutation frequency experiments indicate that combined treatment reduces the generation of resistant mutants within the bacterial population. In summary, PLU can serve as an adjuvant, enhancing the anti-biofilm capability of CHX and reducing the occurrence of resistance mutations, thereby extending the lifespan of CHX.

IMPORTANCE

As disinfectants are extensively and excessively utilized worldwide, clinical pathogens are progressively acquiring resistance against these substances. However, high concentrations of disinfectants can lead to cross-resistance to antibiotics, and concurrent use of different disinfectants can promote bacterial resistance mutations and facilitate the horizontal transfer of resistance genes, which poses significant challenges for clinical treatment. Compared with the lengthy process of developing new disinfectants, enhancing the effectiveness of existing disinfectants with natural plant extracts is important and meaningful. CHX is particularly common and widely used compared with other disinfectants. Meanwhile,
Klebsiella pneumoniae
, as a clinically significant pathogen, exhibits high rates of resistance and pathogenicity. Previous studies and our data indicate a significant decrease in the sensitivity of clinical
K. pneumoniae
to CHX, highlighting the urgent need for novel strategies to address this issue. In light of this, our research is meaningful.
Impact of carbon dioxide concentrations on laboratory sensitivity of
Mycoplasma
species isolated from dairy cows
Authors: Biesheuvel Marit M. , Kalbfleisch Kristen , De Buck Jeroen , van Engelen Erik , van Schaik Gerdien , Moroni Paolo , Gioia Gloria , Nobrega Diego , Samera Gennerick J. , Adams Paul J. , Walcott Jermaine R. , Barkema Herman W. 
Published: August 2024

ABSTRACT

Conventional
Mycoplasma
spp. diagnostics involve culture, often considered the gold standard in diagnostic test evaluation. However, culture protocols lack empirical derivation and primarily adhere to National Mastitis Council recommendations, tracing back to initial cultivation of
Mycoplasma bovis
. Despite a wide range of carbon dioxide (CO
2
) supplementation reported in literature, specific impacts of CO
2
on
Mycoplasma
spp. growth remain unexplored. Our objective was to assess the effect of CO
2
concentration on growth detection rates of 24
Mycoplasma
spp. isolates from dairy cows. These isolates, mainly
M. bovis
, were incubated at 37°C in triplicate and three dilution ranges under three CO
2
conditions: ambient air or 5% CO
2
or 10% CO
2
. Bacterial growth was evaluated on incubation days 3, 5, 7, and 10. When cultured using ambient air, log
10
cfu/mL was lower on days 3, 5, and 7 of incubation compared with isolates incubated in the recommended 5% or 10% CO
2
, with less variation observed in ambient air compared with 5% or 10% CO
2
. However, by 10 days of incubation, no differences in the detection of observable growth were noted among isolates incubated in ambient air, 5% CO
2
, or 10% CO
2
. Consequently,
Mycoplasma
spp. isolated from dairy cattle demonstrated growth after the recommended 7–10 days of culture, even in the absence of supplemental CO
2
. Given the expected concentration of
M. bovis
in (sub)clinical samples had similar concentrations to those used in our study, with the majority of isolates being
M. bovis
, we recommend expanding CO
2
concentration ranges in
M. bovis
culture from 10% CO
2
to ambient air when incubating for 10 days. However, the turnaround time could be shortened when incubating with supplemental CO
2
.

IMPORTANCE

Current
Mycoplasma
spp. culture protocols lack empirical derivation concerning carbon dioxide (CO
2
) supplementation and are primarily based on the initial cultivation of
Mycoplasma bovis
. This study indicates that the suitable range for CO
2
supplementation is broader than what is currently recommended by the National Mastitis Council for culturing within the specified 7–10 days. No differences in bacterial growth detection rates were observed among ambient air, 5% CO
2
, or 10% CO
2
supplementation during the 7- and 10-day incubation intervals. These new insights provide evidence supporting the possibility of culturing
Mycoplasma
spp. under ambient air conditions in a laboratory setting.
Immune gene expression changes more during a malaria transmission season than between consecutive seasons
Authors: Tebben Kieran , Yirampo Salif , Coulibaly Drissa , Koné Abdoulaye K. , Laurens Matthew B. , Stucke Emily M. , Dembélé Ahmadou , Tolo Youssouf , Traoré Karim , Niangaly Amadou , Berry Andrea A. , Kouriba Bourèma , Plowe Christopher V. , Doumbo Ogobara K. , Lyke Kirsten E. , Takala-Harrison Shannon , Thera Mahamadou A. , Travassos Mark A. , Serre David 
Published: August 2024

ABSTRACT

Plasmodium
parasites, the causative organism of malaria, caused over 600,000 deaths in 2022. In Mali,
Plasmodium falciparum
causes the majority of malaria cases and deaths and is transmitted seasonally. Anti-malarial immunity develops slowly over repeated exposures to
P. falciparum
and some aspects of this immunity (e.g., antibody titers) wane during the non-transmission, dry season. Here, we sequenced RNA from 33 pediatric blood samples collected during
P. falciparum
infections at the beginning or end of a transmission season, and characterized the host and parasite gene expression profiles for paired, consecutive infections. We found that human gene expression changes more over the course of one transmission season than between seasons, with signatures of partial development of an adaptive immune response during one transmission season and stability in gene expression during the dry season. Additionally, we found that
P. falciparum
gene expression did not vary with timing during the season and remained stable both across and between seasons, despite varying human immune pressures. Our results provide insights into the dynamics of anti-malarial immune response development over short time frames that could be exploited by future vaccine and prevention efforts.

IMPORTANCE

Our work seeks to understand how the immune response to
Plasmodium falciparum
malaria changes between infections that occur during low and high malaria transmission seasons, and highlights that immune gene expression changes more during the high transmission season. This provides important insight into the dynamics of the anti-malarial immune response that are important to characterize over these short time frames to better understand how to exploit this immune response with future vaccine efforts.
Bile acids activate the antibacterial T6SS1 in the gut pathogen
Vibrio parahaemolyticus
Authors: Schiffmann Sarah , Mass Shir , Salomon Dor 
Published: August 2024

ABSTRACT

The marine bacterium
Vibrio parahaemolyticus
is a major cause of seafood-borne gastroenteritis in humans and of acute hepatopancreatic necrosis disease in shrimp. Bile acids, produced by the host and modified into secondary bile acids by commensal bacteria in the gastrointestinal tract, induce the virulence factors leading to disease in humans and shrimp. Here, we show that secondary bile acids also activate this pathogen’s type VI secretion system 1, a toxin delivery apparatus mediating interbacterial competition. This finding implies that
Vibrio parahaemolyticus
exploits secondary bile acids to activate its virulence factors and identify the presence of commensal bacteria that it needs to outcompete in order to colonize the host.

IMPORTANCE

Bacterial pathogens often manipulate their host and cause disease by secreting toxic proteins. However, to successfully colonize a host, they must also remove commensal bacteria that reside in it and may compete with them over resources. Here, we find that the same host-derived molecules that activate the secreted virulence toxins in a gut bacterial pathogen,
Vibrio parahaemolyticus
, also activate an antibacterial toxin delivery system that targets such commensal bacteria. These findings suggest that a pathogen can use one cue to launch a coordinated,
trans
-kingdom attack that enables it to colonize a host.