Pantoea agglomerans: a mysterious bacterium of evil and good. Part III. Deleterious effects: infections of humans, animals and plants

Human milk microbiome: associations with maternal diet and infant growth

Introduction

Ingestion of human milk (HM) is identified as a significant factor associated with early infant gut microbial colonization, which has been associated with infant health and development. Maternal diet has been associated with the HM microbiome (HMM). However, a few studies have explored the associations among maternal diet, HMM, and infant growth during the first 6 months of lactation.

Methods

For this cross-sectional study, Mam-Mayan mother-infant dyads (n = 64) were recruited from 8 rural communities in the Western Highlands of Guatemala at two stages of lactation: early (6-46 days postpartum, n = 29) or late (109-184 days postpartum, n = 35). Recruited mothers had vaginally delivered singleton births, had no subclinical mastitis or antibiotic treatments, and breastfed their infants. Data collected at both stages of lactation included two 24-h recalls, milk samples, and infant growth status indicators: head-circumference-for-age-z-score (HCAZ), length-for-age-z-score (LAZ), and weight-for-age-z-score (WAZ). Infants were divided into subgroups: normal weight (WAZ ≥ -1SD) and mildly underweight (WAZ < -1SD), non-stunted (LAZ ≥ -1.5SD) and mildly stunted (LAZ < -1.5SD), and normal head-circumference (HCAZ ≥ -1SD) and smaller head-circumference (HCAZ < -1SD). HMM was identified using 16S rRNA gene sequencing; amplicon analysis was performed with the high-resolution ANCHOR pipeline, and DESeq2 identified the differentially abundant (DA) HMM at the species-level between infant growth groups (FDR < 0.05) in both early and late lactation.

Results

Using both cluster and univariate analyses, we identified (a) positive correlations between infant growth clusters and maternal dietary clusters, (b) both positive and negative associations among maternal macronutrient and micronutrient intakes with the HMM at the species level and (c) distinct correlations between HMM DA taxa with maternal nutrient intakes and infant z-scores that differed between breast-fed infants experiencing growth faltering and normal growth in early and late lactation.

Conclusion

Collectively, these findings provide important evidence of the potential influence of maternal diet on the early-life growth of breastfed infants via modulation of the HMM.

Pantoea agglomerans bacteraemia after uterine artery embolisation: an unusual pathogen

A woman in her 40s presented to the emergency department (ED) with a 3-week history of nausea, vomiting and diarrhoea. Blood cultures were positive for Serratia and Pantoea agglomerans spp. One month before her ED visit, she underwent targeted uterine artery embolisation with particles by an interventional radiologist. Uterine artery embolisation is considered a safe alternative to surgical removal of fibroids or hysterectomy. The patient was initially treated with targeted antibiotics for a large infected uterine fibroid but ultimately required a hysterectomy for source control. To our knowledge, this is the first documented case of P. agglomerans infecting a uterine fibroid.

A Rare Organism Causing Cholecystitis With Bacteremia in a Breast Cancer Patient

Pantoea, a gram-negative, rod-shaped, anaerobic bacterium, is a rare cause of human disease. Pantoea species have been known to mostly cause pulmonary disease in agricultural workers as they are native to select crops and wild animal furs. However, in very few documented cases, Pantoea has been discovered as the source of nosocomial infections, usually in the setting of an immunocompromised host. This case report details the clinical course of a 62-year-old immunocompromised female with stage 3 breast cancer presenting with acute cholecystitis and bacteremia and the unexpected discovery of Pantoea in peripheral and chemotherapy port blood cultures. After appropriate management and susceptibility testing, the patient fortunately recovered with initial cefepime and eventual levofloxacin to target the Pantoea species. To our knowledge, this is the third documented case worldwide of Pantoea isolated from cholecystitis with associated bacteremia and the first documented case in North America. Of special interest, a few months after her infection, the patient was found to be free of breast cancer. Pantoea species are known to contain levan, an exopolysaccharide, that has been seen to upregulate tumor suppressor genes. This should be considered in the future management and research of Pantoea infections.

Pantoea Species Bacteremia in a Child With Sickle Cell Disease: A Case Report

The Pantoea genus of bacteria is a group of Gram-negative rod-shaped bacteria in the Enterobacteriaceae family. It is an uncommon cause of infection in humans except in specific settings, including hospital-acquired infections and in immunocompromised patients. In this report, we describe the case of a 12-year-old girl with sickle cell disease who presented with a picture of sepsis and was found to have Pantoea species in her blood culture which was treated with antibiotics with a good response. From our literature review, risk factors were identified in the reported cases, for which further exploration is highly recommended.

Pantoea trifolii sp. nov., a novel bacterium isolated from Trifolium rubens root nodules

A novel bacterium, designated strain MMK2T, was isolated from a surface-sterilised root nodule of a Trifolium rubens plant growing in south-eastern Poland. Cells were Gram negative, non-spore forming and rod shaped. The strain had the highest 16S rRNA gene sequence similarity with P. endophytica (99.4%), P. leporis (99.4%) P. rwandensis (98.8%) and P. rodasii (98.45%). Phylogenomic analysis clearly showed that strain MMK2T and an additional strain, MMK3, should reside in the genus Pantoea and that they were most closely related to P. endophytica and P. leporis. Genome comparisons showed that the novel strain shared 82.96-93.50% average nucleotide identity and 26.2-53. 2% digital DNA:DNA hybridization with closely related species. Both strains produced siderophores and were able to solubilise phosphates. The MMK2T strain was also able to produce indole-3-acetic acid. The tested strains differed in their antimicrobial activity, but both were able to inhibit the growth of Sclerotinia sclerotiorum 10Ss01. Based on the results of the phenotypic, phylogenomic, genomic and chemotaxonomic analyses, strains MMK2T and MMK3 belong to a novel species in the genus Pantoea for which the name Pantoea trifolii sp. nov. is proposed with the type strain MMK2T (= DSM 115063T = LMG 33049T).

Potential airborne human pathogens: A relevant inhabitant in built environments but not considered in indoor air quality standards

Potential airborne human pathogens (PAHPs) may be a relevant component of the air microbiome in built environments. Despite that PAHPs can cause infections, particularly in immunosuppressed patients at medical centers, they are scarcely considered in standards of indoor air quality (IAQ) worldwide. Here, we reviewed the current information on microbial aerosols (bacteria, fungal and viruses) and PAHPs in different types of built environments (e.g., medical center, industrial and non-industrial), including the main factors involved in their dispersion, the methodologies used in their study and their associated biological risks. Our analysis identified the human occupancy and ventilation systems as the primary sources of dispersal of microbial aerosols indoors. We also observed temperature and relative humidity as relevant physicochemical factors regulating the dispersion and viability of some PAHPs. Our analysis revealed that some PAHPs can survive and coexist in different environments while other PAHPs are limited or specific for an environment. In relation to the methodologies (conventional or molecular) the nature of PAHPs and sampling type are pivotal. In this context, indoors air-borne viruses are the less studies because their small size, environmental lability, and absence of efficient sampling techniques and universal molecular markers for their study. Finally, it is noteworthy that PAHPs are not commonly considered and included in IAQ standards worldwide, and when they are included, the total abundance is the single parameter considered and biological risks is excluded. Therefore, we propose a revision, design and establishment of public health policies, regulations and IAQ standards, considering the interactions of diverse factors, such as nature of PAHPs, human occupancy and type of built environments where they develop.

Enterococcus faecium C171: Modulating the Immune Response to Acute Lethal Viral Challenge

Commensal bacteria modulate acute immune responses to infection in hosts. In this study, Enterococcus faecium C171 was screened and isolated. This strain has similar basic characteristics to the reference probiotic, including strong anti-inflammatory and anti-infective effects. E. faecium C171 inhibits the production of pro-Caspase-1 and significantly reduces the production of interleukin-1β (IL-1β) in vitro. These reactions were confirmed using the Transwell system. Live E. faecium C171 mainly exerted an inhibitory effect on acute inflammation, whereas the anti-infective and immune-activating effects were primarily mediated by the E. faecium C171-produced bacterial extracellular vesicles (Efm-C171-BEVs). Furthermore, in the specific pathogen-free (SPF) chicken model, oral administration of E. faecium C171 increased the relative abundance of beneficial microbiota (Enterococcus and Lactobacillus), particularly Enterococcus, the most important functional bacteria of the gut microbiota. E. faecium C171 significantly inhibited the acute inflammatory response induced by a highly virulent infectious disease, and reduced mortality in SPF chickens by 75%. In addition, E. faecium C171 induced high levels of CD3+, CD4-, and CD8- immunoregulatory cells and CD8+ killer T cells, and significantly improved the proliferative activity of T cells in peripheral blood mononuclear cells, and the secretion of interferon-γ. These findings indicate that E. faecium C171 and Efm-C171-BEVs are promising candidates for adjuvant treatment of acute inflammatory diseases and acute viral infections.

Stigmas of holoparasitic Phelipanche arenaria (Orobanchaceae) - a suitable ephemeric flower habitat for development unique microbiome

BACKGROUND

Microbial communities have occasionally been observed in part of the ephemeric reproductive structure of floral stigmas, but their prevalence, phylogenetic diversity and ecological roles are understudied. This report describes the first study of bacterial and fungal communities in immature and mature stigma tissue of the endangered holoparasitic plant Phelipanche arenaria. Culture-dependent methods coupled with next-generation sequencing indicated that a small surface of the flower stigma was an unexpectedly rich and diverse microhabitat for colonization of microbial. We also compared the enzymatic activity of the bacterial communities between immature and mature stigmas samples.

RESULTS

Using high-throughput sequencing methods, we identified and classified 39 to over 51 OTUs per sample for bacterial OTUs represented by Pantoea agglomerans and P. ananatis, comprising 50.6%, followed by Pseudomonas, Luteibacter spp., Sphingomonas spp. with 17% of total frequency. The bacterial profile of immature stigmas of P. arenaria contained unique microorganisms (21 of the most numerous OTUs) that were not confirmed in mature stigmas. However, the enzymatic activity of bacteria in mature stigmas of P. arenaria showed more activity than observed in immature stigmas. In the fungal profile, we recorded even 80 OTUs in mature stigmas, consisting of Capnodiales 45.03% of the total abundance with 28.27% of frequency was created by Alternaria eichhorniae (10.55%), Mycosphaerella tassiana (9.69%), and Aureobasidium pullulans (8.03%). Additionally, numerous putative plant growth-promoting bacteria, fungal pathogens and pathogen-antagonistic yeasts were also detected.

CONCLUSIONS

Our study uncovered that P. arenaria stigmas host diverse bacterial and fungal communities. These microorganisms are well known and have been described as beneficial for biotechnological and environmental applications (e.g., production of different enzymes and antimicrobial compounds). This research provided valuable insight into the parasitic plant-microbe interactions.

Silage preparation and sustainable livestock production of natural woody plant

As the global population increases and the economy grows rapidly, the demand for livestock products such as meat, egg and milk continue to increase. The shortage of feed in livestock production is a worldwide problem restricting the development of the animal industry. Natural woody plants are widely distributed and have a huge biomass yield. The fresh leaves and branches of some woody plants are rich in nutrients such as proteins, amino acids, vitamins and minerals and can be used to produce storage feed such as silage for livestock. Therefore, the development and utilization of natural woody plants for clean fermented feed is important for the sustainable production of livestock product. This paper presents a comprehensive review of the research progress, current status and development prospects of forageable natural woody plant feed resources. The nutritional composition and uses of natural woody plants, the main factors affecting the fermentation of woody plant silage and the interaction mechanism between microbial co-occurrence network and secondary metabolite are reviewed. Various preparation technologies for clean fermentation of woody plant silage were summarized comprehensively, which provided a sustainable production mode for improving the production efficiency of livestock and producing high-quality livestock product. Therefore, woody plants play an increasingly important role as a potential natural feed resource in alleviating feed shortage and promoting sustainable development of livestock product.

Bacteria intrinsic to Medicago sativa (alfalfa) reduce Salmonella enterica growth in planta

AIMS

The purpose of this study was to determine whether plant-associated bacteria (PAB) can reduce Salmonella enterica colonization and infection of alfalfa sprouts to reduce the risk of foodborne illness.

METHODS

We isolated PAB from alfalfa seeds and sprouts. Monoclonal isolates of the bacteria were obtained and tested for their ability to inhibit Salmonella Typhimurium growth in alfalfa sprouts over 6 days. Genome sequencing and annotation were used to construct draft genomes of the bacteria isolated in this study using Illumina sequencing platform.

RESULTS

We observed that a cocktail of five PAB could reduce Salmonella growth in alfalfa sprouts from ∼108 to ∼105 CFU g-1, demonstrating a protective role. Genome sequencing revealed that these bacteria were members of the Pseudomonas, Pantoea, and Priestia genus, and did not possess genes that were pathogenic to plants or animals.

CONCLUSIONS

This work demonstrates that PAB can be utilized to reduce pathogen levels in fresh produce, which may be synergistic with other technologies to improve the safety of sprouts and other fresh produce.

Genomic characterization of Pantoea anthophila strain UI705 causing urinary tract infections in China

Introduction

Pantoea anthophila (P. anthophila) is a Gram-negative bacterium initially isolated from Impatiens balsamina in India. P. anthophila has been characterized with low pathogenicity, and no human infections caused by this organism have been reported yet. We report the first case of urinary tract infection caused by P. anthophila in a 73-year-old man after bladder cancer surgery.

Methods

The bacterial isolate gained from urine was named UI705 and identified as P. anthophila by MALDI-TOF mass spectrometry. The genome sequencing and analysis were performed to further characterize the pathogenesis of the clinical isolate.

Result and discussion

To the best of our knowledge, this is the first report of human infection caused by P. anthophila in China. The draft genome sequence of P. anthophila UI705 provides a fundamental resource for subsequent investigation of its virulence factors, antibiotic resistance, host-pathogen interactions, and comparative genomics of genus Pantoea.

Culturomics and Circular Agronomy: Two Sides of the Same Coin for the Design of a Tailored Biofertilizer for the Semi-Halophyte Mesembryanthemum crystallinum

According to the EU, the global consumption of biomass, fossil fuels, metals, and minerals is expected to double by 2050, while waste will increase by 70%. In this context, the Circular Economy Action Plan (CEAP) intends to integrate development and sustainability. In this regard, tailored biofertilizers based on plant growth-promoting bacteria (PGPB) can improve plant yield with fewer inputs. In our project, an autochthonous halophyte of the Andalusian marshes, namely Mesembryanthemum crystallinum, was selected for its interest as a source of pharmaceuticals and nutraceuticals. The aim of this work was to use a culturomics approach for the isolation of specific PGPB and endophytes able to promote plant growth and, eventually, modulate the metabolome of the plant. For this purpose, a specific culture medium based on M. crystallinum biomass, called Mesem Agar (MA), was elaborated. Bacteria of three compartments (rhizosphere soil, root endophytes, and shoot endophytes) were isolated on standard tryptone soy agar (TSA) and MA in order to obtain two independent collections. A higher number of bacteria were isolated on TSA than in MA (47 vs. 37). All the bacteria were identified, and although some of them were isolated in both media (Pseudomonas, Bacillus, Priestia, Rosellomorea, etc.), either medium allowed the isolation of specific members of the M. crystallinum microbiome such as Leclercia, Curtobacterium, Pantoea, Lysinibacillus, Mesobacillus, Glutamicibacter, etc. Plant growth-promoting properties and extracellular degrading activities of all the strains were determined, and distinct patterns were found in both media. The three best bacteria of each collection were selected in order to produce two different consortia, whose effects on seed germination, root colonization, plant growth and physiology, and metabolomics were analyzed. Additionally, the results of the plant metabolome revealed a differential accumulation of several primary and secondary metabolites with pharmaceutical properties. Overall, the results demonstrated the feasibility of using "low cost media" based on plant biomass to carry out a culturomics approach in order to isolate the most suitable bacteria for biofertilizers. In this way, a circular model is established in which bacteria help plants to grow, and, in turn, a medium based on plant wastes supports bacterial growth at low prices, which is the reason why this approach can be considered within the model of "circular agronomy".

Prevalence of Culturable Bacteria and Yeasts in the Nasopharynx Microbiota during the Physiological Course of Pregnancy

The aim of the study was to compare the prevalence of the nasopharyngeal carriage of culturable microorganisms in the microbiota of asymptomatic women with a physiological pregnancy (PW) and nonpregnant women (NPW). Nasopharyngeal swabs were collected from 53 PW and 30 NPW to detect bacterial and fungal colonization. Isolates were identified using the culture method and the MALDI-TOF MS technique. The nasopharyngeal microbiota (NPM) partially differed between PW and NPW. These differences in the frequency of nasopharyngeal colonization between the PW and NPW groups were not statistically significant (p > 0.05); all cases were colonized by bacteria and only two cases in the PW group were colonized by yeasts, namely, Rhodotorula spp. High levels of staphylococcal colonization, including predominantly coagulase-negative staphylococci and S. aureus in the nasopharyngeal sample, were present in both groups. The reduced number of Gram-negative rods colonized in the cases studied was seen in samples from the NPW group, particularly with Enterobacterales, and anaerobic Cutibacterium spp. were isolated only in the PW group (p < 0.05). Moreover, a higher carriage rate of Enterobacter aerogenes colonization was statistically significant (p < 0.05) and correlated with the NPW group. Pregnancy may disturb the composition of the NPM represented by commensals and opportunistic bacteria and promote yeast colonization as compared to nonpregnant women.

Complete Genome Sequence of Pantoea stewartii RON18713 from Brazil Nut Tree Phyllosphere Reveals Genes Involved in Plant Growth Promotion

The Amazonian rainforest is a hyper-diverse ecosystem in the number of species and the myriad of intertaxon relationships that are mostly understudied. In order to characterize a dominant and economically important Amazonian species, the Brazil nut tree (Bertholletia excelsa Bonpl.), at the genome level, wegenerated high-coverage long-read sequencing data from the leaves of a single individual. The genome assembly revealed an unexpected discovery: two circular contigs that could be assigned to the chromosome and a plasmid of a Pantoea stewartii strain. Comparative genomics revealed that this strain belongs to the indologenes subspecies and displays high synteny with other strains isolated from diseased leaves of the neotropical palm Bactris gasipaes Kunth. Investigation of pathogenicity-related genes revealed the absence of the entire type III secretion system gene cluster in the plasmid, which was otherwise highly similar to a plasmid from an isolate known to cause disease in Dracaena sanderiana Mast. In contrast, several genes associated with plant-growth promoting traits were detected, including genes involved in indole-3-acetic acid (IAA) production, phosphate solubilization, and biosynthesis of siderophores. In summary, we report the genome of an uncultivated P. stewartii subsp. indologenes strain associated with the Brazil nut tree and potentially a plant growth-promoting bacteria.

Mirror proteorhodopsins

Proteorhodopsins (PRs), bacterial light-driven outward proton pumps comprise the first discovered and largest family of rhodopsins, they play a significant role in life on the Earth. A big remaining mystery was that up-to-date there was no described bacterial rhodopsins pumping protons at acidic pH despite the fact that bacteria live in different pH environment. Here we describe conceptually new bacterial rhodopsins which are operating as outward proton pumps at acidic pH. A comprehensive function-structure study of a representative of a new clade of proton pumping rhodopsins which we name "mirror proteorhodopsins", from Sphingomonas paucimobilis (SpaR) shows cavity/gate architecture of the proton translocation pathway rather resembling channelrhodopsins than the known rhodopsin proton pumps. Another unique property of mirror proteorhodopsins is that proton pumping is inhibited by a millimolar concentration of zinc. We also show that mirror proteorhodopsins are extensively represented in opportunistic multidrug resistant human pathogens, plant growth-promoting and zinc solubilizing bacteria. They may be of optogenetic interest.

Diverse Virulence Attributes of Pantoea alfalfae sp. nov. CQ10 Responsible for Bacterial Leaf Blight in Alfalfa Revealed by Genomic Analysis

Alfalfa is widely grown worldwide for its excellent nutritional value. Pantoea species living in alfalfa seeds can easily spread over great distances with frequent trade. However, the pathogenic properties of this dangerous hitchhiker on alfalfa have not been evaluated. Here, we identified the taxonomic status of Pantoea strain CQ10 isolated from the interior of alfalfa seeds based on the whole genome sequence. The diverse virulence attributes of strain CQ10 during host infection were characterized through pathogenicity assays and functional and genomic analyses. We report that strain CQ10 belongs to a novel species in the genus Pantoea, which was phylogenetically close to Pantoea vagans and Pantoea agglomerans. Strain CQ10 caused bacterial leaf blight of alfalfa after inoculation from the roots. We found that strain CQ10 possesses a large number of pathogenic genes involved in shaping the virulence properties during bacteria-host interactions, including motility, biofilm, type VI secretion system, and nutrient acquisition. Compared with P. vagans and P. agglomerans, the unique virulence factors of strain CQ10 were mainly involved in motility and biofilm, which were confirmed by in vitro experiments. Taken together, our results suggest that strain CQ10 is the first Pantoea species to infect alfalfa, and it possesses diverse virulence attributes among which motility and biofilm may be the best weapons.

Pantoea abscess mimicking sarcoma in a HTLV-1-infected Indigenous Australian man: Case report and literature review

Gram-negative bacteria of the genus Pantoea are emerging bacterial causes of diverse sporadic and outbreak-linked infections. Chronic Pantoea abscesses are unusual and may give rise to a differential diagnosis of malignancy. Foreign body retention and host immune defects may be risk factors for such chronic infections.

Microbiota Assessment of Fresh-Cut Apples Packaged in Two Different Films

The aim of this work was to assess the natural microbiota of packed fresh-cut apples during refrigerated storage. Two different films were tested for the package, a biodegradable (PLA) film and a conventional and commercial one (OPP). Two antioxidant additives were applied, a natural olive pomace extract and the commercial ascorbic acid used by the industries. The results revealed lower bacteria counts in samples with olive pomace extract and PLA films than in those with ascorbic acid and OPP films after 5 and 12 days of storage. These findings suggest that the use of such natural extracts as additives in fruits could delay the growth of mesophilic bacteria. The characterization and identification of the bacterial isolates from fresh-cut apple samples showed that the most prevalent species were Citrobacter freundii, Staphylococcus warneri, Pseudomonas oryzihabitans, Alcalinogenes faecalis, Corynebacterium jeikeium, Micrococcus spp., Pantoea aglomerans and Bacillus spp. Furthermore, an increase in the microbial diversity during the storage time at refrigerated temperatures was observed, except for the sample treated with olive pomace extract and packaged in OPP film. The highest microbial diversity was found for samples with ascorbic acid as an additive. This could indicate a negative effect of ascorbic acid on the microbial inhibition of apple slices. The natural olive pomace extract demonstrated potential as an antimicrobial additive for fresh-cut apples.

First Study on profiling of gut microbiome in wild and captive Sumatran orangutans (Pongo abelii)

Background and Aim

Orangutans are an "umbrella species" for conserving tropical forests in Sumatra and Kalimantan. There are remarkable changes between the gut microbiomes of wild and captive Sumatran orangutans. This study aimed to profile gut microbiota of wild and captive Sumatran orangutans.

Materials and Methods

Nine fecal samples collected from wild orangutans and nine fecal samples collected from captive orangutans were divided into three replicates. Each replicate randomly combined three pieces and were analyzed on the Illumina platform. A bioinformatics study of 16S rRNA according to Qiime2 (Version 2021.4) and microbiome profiling analysis was conducted.

Results

The relative abundance of different microbial taxa varied significantly between wild and captive Sumatran orangutans. Among the operational taxonomic units, various proportions of Firmicutes, Proteobacteria, Bacteroidetes, Euryarchaeota, Acidobacteria, Actinobacteria and Verrucomicrobia predominated. Solobacterium was found only in 19% of captive orangutans. Methanobrevibacter was identified to be prevalent among wild orangutans (16%). Analysis of the core microbiome from the combined wild and captive data revealed seven species as cores. According to linear discriminant analysis effect size, Micrococcus luteus, Bacteroidescaccae, Lachnospiraceae bacterium, Ruthenibacterium lactatiformans, Haemophilus haemolyticus, and Chishuiella spp. were microbiome biomarkers in captive orangutans, whereas Roseburia inulinivorans, Collinsella aerofaciens, Oscillibacter spp., and Eubacterium hallii were microbiome biomarkers in wild orangutans.

Conclusion

There were differences in the microbiome biomarkers of wild and captive Sumatran orangutans. This study is important for understanding the role of gut bacteria in the health of Sumatran orangutans.

Whole-Genome Sequence of Endophytic Bacteria Associated with Poison Ivy Vine (Toxicodendron radicans)

Here, we report the genome assemblies of 11 endophytic bacteria, isolated from poison ivy vine (Toxicodendron radicans). Five species belonging to the genus Pseudomonas, two species of Curtobacterium, one strain of Pantoea agglomerans, and one species from the Bacillus, Cellulomonas, and Enterobacter genera were isolated from the interior tissue of poison ivy.

Epiphitic Microbiome of Alvarinho Wine Grapes from Different Geographic Regions in Portugal

Geographic location and, particularly, soil and climate exert influence on the typicality of a wine from a specific region, which is often justified by the terroir, and these factors also influence the epiphytic flora associated with the surface of the grape berries. In the present study, the microbiome associated with the surface of berries obtained from ten vineyards of the Alvarinho variety located in different geographical locations in mainland Portugal was determined and analyzed. The removal of microbial flora from the surface of the berries was carried out by washing and sonication, after which the extraction and purification of the respective DNA was carried out. High-throughput short amplicon sequencing of the fungal ITS region and the bacterial 16S region was performed, allowing for the determination of the microbial consortium associated with Alvarinho wine grapes. Analysis of α-diversity demonstrated that parcels from the Monção and Melgaço sub-region present a significantly (p < 0.05) lower fungal diversity and species richness when compared to the plots analyzed from other regions/sub-regions. The ubiquitous presence of Metschnikowia spp., a yeast with enologic potential interest in all parcels from Monção and Melgaço, was also observed.

Three Phages One Host: Isolation and Characterization of Pantoea agglomerans Phages from a Grasshopper Specimen

The bacterial genus Pantoea comprises species found in a variety of different environmental sources. Pantoea spp. are often recovered from plant material and are capable of both benefitting the plants and acting like phytopathogens. Some species of Pantoea (including P. agglomerans) are considered opportunistic human pathogens capable of causing various infections in immunocompromised subjects. In this study, a strain of P. agglomerans (identified by 16S rRNA gene sequencing) was isolated from a dead specimen of an unidentified Latvian grasshopper species. The retrieved strain of P. agglomerans was then used as a host for the potential retrieval of phages from the same source material. After rounds of plaque purification and propagation, three high-titer lysates corresponding to putatively distinct phages were acquired. Transmission electron microscopy revealed that one of the phages was a myophage with an unusual morphology, while the two others were typical podophages. Whole-genome sequencing (WGS) was performed for each of these isolated phages. Genome de novo assembly and subsequent functional annotation confirmed that three different strictly lytic phages were isolated. Elaborate genomic characterization of the acquired phages was performed to elucidate their place within the so-far-uncovered phage diversity.

Surveillance in a Neonatal Intensive Care Unit Allowed the Isolation of a Strain of VIM-Producing Pantoea brenneri

Here, we describe the isolation of a strain of the genus Pantoea encoding a VIM carbapenemase, the first to our knowledge. The strain, isolated from a rectal swab of a 10-day-old newborn admitted to a neonatal intensive care unit (NICU), was identified through whole-genome sequencing analyses as Pantoea brenneri. The strain harbored the carbapenemases gene bla_VIM-1. The prompt application of contact measures and the isolation of the newborn prevented the dissemination of VIM-producing P. brenneri and of the plasmid carrying the VIM-1 gene to other newborns.

Optimization of the growth conditions through response surface methodology and metabolomics for maximizing the auxin production by Pantoea agglomerans C1

Introduction

The fermentative production of auxin/indole 3-acetate (IAA) using selected Pantoea agglomerans strains can be a promising approach to developing novel plant biostimulants for agriculture use.

Methods

By integrating metabolomics and fermentation technologies, this study aimed to define the optimal culture conditions to obtain auxin/IAA-enriched plant postbiotics using P. agglomerans strain C1. Metabolomics analysis allowed us to demonstrate that the production of a selected.

Results and discussion

Array of compounds with plant growth-promoting- (IAA and hypoxanthine) and biocontrol activity (NS-5, cyclohexanone, homo-L-arginine, methyl hexadecenoic acid, and indole-3-carbinol) can be stimulated by cultivating this strain on minimal saline medium amended with sucrose as a carbon source. We applied a three-level-two-factor central composite design (CCD) based response surface methodology (RSM) to explore the impact of the independent variables (rotation speed and medium liquid-to-flask volume ratio) on the production of IAA and IAA precursors. The ANOVA component of the CCD indicated that all the process-independent variables investigated significantly impacted the auxin/IAA production by P. agglomerans strain C1. The optimum values of variables were a rotation speed of 180 rpm and a medium liquid-to-flask volume ratio of 1:10. Using the CCD-RSM method, we obtained a maximum indole auxin production of 208.3 ± 0.4  mg IAA_equ/L, which was a 40% increase compared to the growth conditions used in previous studies. Targeted metabolomics allowed us to demonstrate that the IAA product selectivity and the accumulation of the IAA precursor indole-3-pyruvic acid were significantly affected by the increase in the rotation speed and the aeration efficiency.

Bacterial diversity of hospital water tanks and the efficacy of hydrogen peroxide based cleaning: Experience in a tertiary care center in India

BACKGROUND

Hospital water is often an overlooked yet preventable source of hospital-acquired infections. CDC recommends annual cleaning of water reservoirs in health care settings. In our tertiary care hospital, periodic disinfection and microbiological surveillance of all the water tanks in hospital premises is carried out. The aim of this paper is to report the diversity of bacterial flora noted and the role of cleaning method adopted in our hospital.

METHODS

This retrospective study was carried out from July 2015 to September 2020. Tanks were cleaned using hydrogen peroxide based method and swabs were collected, pre- and post-cleaning. Any growth noted was identified using MALDI-TOF MS.

RESULTS

A total of 398 swabs were collected during this period. In pre-cleaning samples, 144 (72%) showed growth of 219 microorganisms. Gram-negative organisms (53.7%, 116/216) were more frequently isolated than Gram-positive organisms (46.3%, 100/216). Although the overwhelming majority is generally regarded as non-pathogenic, a few pathogenic bacteria were also recovered. No bacteria were isolated in any of the post-cleaning samples.

CONCLUSIONS

Diverse bacteria colonize water tanks over time, some of which are known to cause infections. Hydrogen peroxide is a simple and highly efficacious method of water tank disinfection. More such studies are required with other disinfectants to generate evidence with the ultimate aim of increasing safety of water supplied in hospitals.

Hymenolepis diminuta Reduce Lactic Acid Bacterial Load and Induce Dysbiosis in the Early Infection of the Probiotic Colonization of Swiss Albino Rat

Tapeworm infection continues to be an important cause of morbidity worldwide. Recent metagenomics studies have established a link between gut microbiota and parasite infection. The identification of gut probiotics is of foremost importance to explore its relationship and function with the parasite in the host. In this study, the gut content of hosts infected with tapeworm Hymenolepis diminuta and non-infected host gut were disected out to determine their Lactic acid bacterial (LAB) population in MRS agar and microbial community was analysed by metagenomics. The bacterial count was calculated on a bacterial counting chamber and their morphology was determined microscopically and biochemically. Further, to determine the safety profile antibiotic resistance test, antimicrobial, hemolytic activity, and adhesion capability were calculated. We found six dominant probiotic strains and a decrease in LAB load from 1.7-2.3 × 10⁷ CFU/mL in the uninfected group to a range of 8.4 × 10⁵ CFU/mL to 3.2 × 10⁵ CFU/mL in the infected groups with respect to an increase in the parasite number from 10-18. In addition, we found a depletion in the probiotic relative abundance of Lactobacillus and an enrichment in potentially pathogenic Proteobacteria, Fusobacteria, and Streptococcus. Phylogenetic analysis of the six probiotics revealed a close similarity with different strains of L. brevis, L. johnsonii, L. taiwansis, L. reuteri, L. plantarum, and L. pentosus. Thus, this study suggests that the parasite inhibits probiotic colonization in the gut during its early establishment of infection inside the host.

Human milk microbial species are associated with infant head-circumference during early and late lactation in Guatemalan mother-infant dyads

Human milk contains abundant commensal bacteria that colonize and establish the infant's gut microbiome but the association between the milk microbiome and head circumference during infancy has not been explored. For this cross-sectional study, head-circumference-for-age-z-scores (HCAZ) of vaginally delivered breastfed infants were collected from 62 unrelated Mam-Mayan mothers living in eight remote rural communities in the Western Highlands of Guatemala during two stages of lactation, 'early' (6-46 days postpartum, n = 29) or 'late' (109-184 days postpartum, n = 33). At each stage of lactation, infants were divided into HCAZ ≥ -1 SD (early: n = 18; late: n = 14) and HCAZ < -1 SD (early: n = 11; late: n = 19). Milk microbiome communities were assessed using 16S ribosomal RNA gene sequencing and DESeq2 was used to compare the differential abundance (DA) of human milk microbiota with infant HCAZ subgroups at both stages of lactations. A total of 503 ESVs annotated 256 putative species across the 64 human milk samples. Alpha-diversity using Chao index uncovered a difference in microbial community richness between HCAZ ≥ -1 SD and HCAZ < -1 SD groups at late lactation (p = 0.045) but not at early lactation. In contrast, Canonical Analysis of Principal Coordinates identified significant differences between HCAZ ≥ -1 SD and HCAZ < -1 SD at both stages of lactation (p = 0.003); moreover, 26 milk microbial taxa differed in relative abundance (FDR < 0.05) between HCAZ ≥ -1 SD and HCAZ < -1 SD, with 13 differentially abundant at each lactation stage. Most species in the HCAZ ≥ -1 SD group were Streptococcus species from the Firmicutes phylum which are considered human colonizers associated with human milk whereas the HCAZ < -1 SD group at late lactation had more differentially abundant taxa associated with environmentally and 'potentially opportunistic' species belonging to the Actinobacteria genus. These findings suggest possible associations between brain growth of breastfed infants and the milk microbiome during lactation. Importantly, these data provide the first evidence of cross talk between the human milk microbiome and the infant brain that requires further investigation.

Opposite Sides of Pantoea agglomerans and Its Associated Commercial Outlook

Multifaceted microorganisms such as the bacterium Pantoea colonize a wide range of habitats and can exhibit both beneficial and harmful behaviors, which provide new insights into microbial ecology. In the agricultural context, several strains of Pantoea spp. can promote plant growth through direct or indirect mechanisms. Members of this genus contribute to plant growth mainly by increasing the supply of nitrogen, solubilizing ammonia and inorganic phosphate, and producing phytohormones (e.g., auxins). Several other studies have shown the potential of strains of Pantoea spp. to induce systemic resistance and protection against pests and pathogenic microorganisms in cultivated plants. Strains of the species Pantoea agglomerans deserve attention as a pest and phytopathogen control agent. Several of them also possess a biotechnological potential for therapeutic purposes (e.g., immunomodulators) and are implicated in human infections. Thus, the differentiation between the harmful and beneficial strains of P. agglomerans is mandatory to apply this bacterium safely as a biofertilizer or biocontroller. This review specifically evaluates the potential of the strain-associated features of P. agglomerans for bioprospecting and agricultural applications through its biological versatility as well as clarifying its potential animal and human health risks from a genomic point of view.

Effects of autochthonous strains mixture on gut microbiota and metabolic profile in cobia (Rachycentron canadum)

The fish immune system is a topic or subject that offers a unique understanding of defensive system evolution in vertebrate heredity. While gut microbiota plays several roles in fish: well-being, promoting health and growth, resistance to bacterial invasion, regulation of energy absorption, and lipid metabolism. However, studies on fish gut microbiota face practical challenges due to the large number of fish varieties, fluctuating environmental conditions, and differences in feeding habits. This study was carried out to evaluate the impacts of supplemented three autochthonous strains, Bacillus sp. RCS1, Pantoea agglomerans RCS2, and Bacillus cereus RCS3 mixture diet on cobia fish (Rachycentron canadum). Also, chromatography, mass spectrometry and high throughput sequencing were combined to explore composition and metabolite profile of gut microbiota in juvenile cobia fed with supplemented diet. In the trial group, juvenile cobia received diets supplemented with 1 × 10¹² CFU mL^-1 autochthonous strains for ten weeks and a control diet without supplementation. Juvenile cobia receiving diets supplementation exhibited significantly improved growth than those without additives (control). Haematological indices, such as red blood cells, white blood cells, corpuscular haemoglobin concentration, mean corpuscular volume, haemoglobin, and mean corpuscular haemoglobin, were higher in the supplemented group. Similarly, digestive enzymes (trypsin, lipase, amylase, pepsin and cellulose, activities) activities were higher in supplemented diet with an indigenous isolates mixture. Serum biochemical parameters albumin, globulin, and total protein were significantly higher, while triglyceride, alanine aminotransferase, aspartate aminotransferase, alkaline phosphatase, and cholesterol showed no significant difference. On the other hand, glucose was significantly (P < 0.05) higher in the group without supplementation. On gene expression in the midgut, Immunoglobulin, Colony-stimulating factor receptor 1, major histocompatibility complex 1 were up-regulated by native isolates while T cell receptor beta, and Major histocompatibility complex 2 showed no significant difference. Gut bacterial composition was altered in fish receiving supplemented diet with autochthonous strains. Metabolomics also revealed that some metabolic pathways were considerably enriched in fish fed with supplemented diet; pathway analysis based on Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment revealed that differentially expressed metabolites were involved in galactose metabolism, tryptophan metabolism, carbohydrate digestion and absorption, purine metabolism, and ABC transporters. Functional analysis of bacterial community showed that differences in enriched metabolic pathways generally comprised carbohydrate and its metabolites, nucleotide and its metabolites, amino acid and its metabolites, heterocyclic compounds, and tryptamines, cholines, pigments. The current investigation results showed that autochthonous strains mixture has significantly enhanced the growth, survival, and innate and adaptive immunities of juvenile cobia.

First report of bacterial wilt disease caused by Pantoea agglomerans on the ornamental perennial Oxalis articulata in China

Oxalis articulata is now widely cultivated in China as an ornamental species, and thus found in abundance in agricultural farms, gardens, and lawns. In December 2021, some severely infected Oxalis articulata were observed at many places at Zhejiang Normal University (29°8'4″N, 119°37'54″E) in Jinhua City, Zhejiang Province, China. Yellow was first observed on the margin of the leaves, leading to light brown and wilting at a later stage. To identify the pathogen, symptomatic leaves were collected and cut into small pieces, surface disinfected in 1% sodium hypochlorite solution for 3 min, followed by 75% alcohol for 0.5 min, then rinsed in sterile distilled water thrice. Then they were transferred onto Luria-Bertani medium and incubated at 28°C for 3 days. The colonies were round, yellow, viscous and smooth, which was consistent with the characteristics of Pantoea agglomerans (Li et al. 2020; Zhang et al. 2022). The bacteria tested gram-negative, negative for indole test and Voges-Proskauer reaction, and positive for methyl red reaction, lysine decarboxylase and ornithine decarboxylase. In addition, the bacteria can utilize D-xylose, sorbitol, adonitol, and glucose, but can't utilize raffinose, urea, and Simmons. Meanwhile the bacteria can not produce H2S, and can not produce gas from D-glucose as well. These results of physiological and biochemical characteristics were consistent with those of Pantoea agglomerans (Gavini et al. 1989). To identify the strain, the 16S rDNA gene fragment was amplified by polymerase chain reaction (PCR) using universal primers 8F and 1510R, and sequenced. The BLAST results indicated that the 16S rDNA sequence of the strain OAPB-1, deposited under GenBank accession LC709256, showed 99.93% (1376/1377) and 99.49% (1370/1377) identity to the corresponding sequence of Pantoea agglomerans FC2948 (MH532498.1) and the type strain Pantoea agglomerans DSM 3493 (AJ233423) respectively. The Neighbor-Joining phylogenetic tree generated using MEGA11 indicated that it formed a clade with the other P. agglomerans. Furthermore, the phylogenetic analysis based on sequences of housekeeping genes (atpD, rpoB and infB; GenBank accession LC722492 to LC722494) showed the same result. Based on the above results, the strain OAPB-1 from Zhejiang was identified as P.agglomerans. To test the Koch's postulates, bacterial suspensions (2×108CFU/mL) were injected into the middle of healthy leaves of mature plants with sterile water as a control. Then the plants were placed at 28°C in a light incubator with 12-h-light/12-h-dark photoperiod and approximately 60% humidity. Leaves in the inoculated group showed symptoms similar to those observed on the naturally infected leaves, while leaves in the control group showed no symptoms. The pathogen was reisolated from inoculated leaves, and its morphological characteristics and molecular identification results were consistent with those of the original isolate. P. agglomerans is a bacterium associated with plants, and also infects humans and animals (Dutkiewicz et al. 2016). In China, it has been reported to infect many kinds of plants (Fan et al. 2022; Guo et al. 2020; Han et al. 2020; Li et al. 2020; She et al. 2019; Zhang et al. 2022). As far as we know, this is the first report of P. agglomerans causing bacterial wilt on Oxalis articulata in China. These results further expand the range of plants that can be infected by P. agglomerans, and help to establish an effective control strategy against the disease.

Beneficial Effect and Potential Risk of Pantoea on Rice Production

Bacteria from the genus Pantoea have been reported to be widely distributed in rice paddy environments with contradictory roles. Some strains promoted rice growth and protected rice from pathogen infection or abiotic stress, but other strain exhibited virulence to rice, even causing severe rice disease. In order to effectively utilize Pantoea in rice production, this paper analyzed the mechanisms underlying beneficial and harmful effects of Pantoea on rice growth. The beneficial effect of Pantoea on rice plants includes growth promotion, abiotic alleviation and disease inhibition. The growth promotion may be mainly attributed to nitrogen-fixation, phosphate solubilization, plant physiological change, the biosynthesis of siderophores, exopolysaccharides, 1-aminocyclopropane-1-carboxylic acid deaminase and phytohormones, including cytokinin, indole-3-acetic acid (IAA), auxins, abscisic acid and gibberellic acid, while the disease inhibition may be mainly due to the induced resistance, nutrient and spatial competition, as well as the production of a variety of antibiotics. The pathogenic mechanism of Pantoea can be mainly attributed to bacterial motility, production of phytohormones such as IAA, quorum sensing-related signal molecules and a series of cell wall-degrading enzymes, while the pathogenicity-related genes of Pantoea include genes encoding plasmids, such as the pPATH plasmid, the hypersensitive response and pathogenicity system, as well as various types of secretion systems, such as T3SS and T6SS. In addition, the existing scientific problems in this field were discussed and future research prospects were proposed.

Bitter friends are not always toxic: The loss of acetic acid bacteria and the absence of Komagataeibacter in the gut microbiota of the polyphagous fly Anastrepha ludens could inhibit its development in Psidium guajava in contrast to A. striata and A. fraterculus that flourish in this host

The gut microbiota is key for the homeostasis of many phytophagous insects, but there are few studies comparing its role on host use by stenophagous or polyphagous frugivores. Guava (Psidium guajava) is a fruit infested in nature by the tephritids Anastrepha striata and A. fraterculus. In contrast, the extremely polyphagous A. ludens infests guava only under artificial conditions, but unlike A. striata and the Mexican A. fraterculus, it infests bitter oranges (Citrus x aurantium). We used these models to analyze whether the gut microbiota could explain the differences in host use observed in these flies. We compared the gut microbiota of the larvae of the three species when they developed in guava and the microbiota of the fruit pulp larvae fed on. We also compared the gut microbiota of A. ludens developing in C. x aurantium with the pulp microbiota of this widely used host. The three flies modified the composition of the host pulp microbiota (i.e., pulp the larvae fed on). We observed a depletion of Acetic Acid Bacteria (AAB) associated with a deleterious phenotype in A. ludens when infesting P. guajava. In contrast, the ability of A. striata and A. fraterculus to infest this fruit is likely associated to a symbiotic interaction with species of the Komagataeibacter genus, which are known to degrade a wide spectrum of tannins and polyphenols. The three flies establish genera specific symbiotic associations with AABs. In the case of A. ludens, the association is with Gluconobacter and Acetobacter, but importantly, it cannot be colonized by Komagataeibacter, a factor likely inhibiting its development in guava.

Microbial community dispersal from wheat grains to sourdoughs : a contribution of participatory research

Understanding microbial dispersal is critical to understand the dynamics and evolution of microbial communities. However, microbial dispersal is difficult to study because of uncertainty about their vectors of migration. This applies to both microbial communities in natural and human-associated environments. Here, we studied microbial dispersal along the sourdoughs bread making chain using a participatory research approach. Sourdough is a naturally fermented mixture of flour and water. It hosts a community of bacteria and yeasts whose origins are only partially known. We analysed the potential of wheat grains and flour to serve as an inoculum for sourdough microbial communities using 16S rDNA and ITS1 metabarcoding. First, in an experiment involving farmers, a miller and bakers, we followed the microbiota from grains to newly initiated and propagated sourdoughs. Second, we compared the microbiota of 46 sourdough samples collected everywhere in France, and of the flour used for their backslopping. The core microbiota detected on the seeds, in the flour and in the sourdough was composed mainly of microbes known to be associated with plants and not living in sourdoughs. No sourdough yeast species were detected on grains and flours. Sourdough lactic acid bacteria were rarely found in flour. When they were, they did not have the same amplicon sequence variant (ASV) as found in the corresponding sourdough. However, the low sequencing depth for bacteria in flour did not allow us to draw definitive conclusion. Thus, our results showed that sourdough yeasts did not come from flour, and suggest that neither do sourdough LAB.

Tardigrade Community Microbiomes in North American Orchards Include Putative Endosymbionts and Plant Pathogens

The microbiome of tardigrades, a phylum of microscopic animals best known for their ability to survive extreme conditions, is poorly studied worldwide and completely unknown in North America. An improved understanding of tardigrade-associated bacteria is particularly important because tardigrades have been shown to act as vectors of the plant pathogen Xanthomonas campestris in the laboratory. However, the potential role of tardigrades as reservoirs and vectors of phytopathogens has not been investigated further. This study analyzed the microbiota of tardigrades from six apple orchards in central Iowa, United States, and is the first analysis of the microbiota of North American tardigrades. It is also the first ever study of the tardigrade microbiome in an agricultural setting. We utilized 16S rRNA gene amplicon sequencing to characterize the tardigrade community microbiome across four contrasts: location, substrate type (moss or lichen), collection year, and tardigrades vs. their substrate. Alpha diversity of the tardigrade community microbiome differed significantly by location and year of collection but not by substrate type. Our work also corroborated earlier findings, demonstrating that tardigrades harbor a distinct microbiota from their environment. We also identified tardigrade-associated taxa that belong to genera known to contain phytopathogens (Pseudomonas, Ralstonia, and the Pantoea/Erwinia complex). Finally, we observed members of the genera Rickettsia and Wolbachia in the tardigrade microbiome; because these are obligate intracellular genera, we consider these taxa to be putative endosymbionts of tardigrades. These results suggest the presence of putative endosymbionts and phytopathogens in the microbiota of wild tardigrades in North America.

Prevalence and characterization of Ice Nucleation Active (INA) bacteria from rainwater in Indonesia

Background

Ice nucleation active (INA) bacteria are a group of microorganisms that can act as biological nucleator due to their ice nucleation protein property. Unfortunately, little is known about their prevalence and characteristics in tropical areas including Indonesia. Here, we monitor the presence of INA bacteria in rainwater and air samples collected from Jakarta, Tangerang and several areas in Western Java, Indonesia for one year. We further identify and characterize selected Class A of INA bacteria isolated from these areas.

Results

Most of the INA bacteria were isolated from rainwater samples collected during March–August 2010, particularly from Jakarta, Bandung, and Tangerang. A total of 1,902 bacterial isolates were recovered from these area. We found a limited number of bacterial isolates from air sampling. From ice nucleation activity assays, 101 INA isolates were found active as ice nucleator at a temperature above -10 °C. A large majority (73 isolates) of them are classified as Class C (active below -8 °C), followed by Class A (26 isolates; active at -2 to -5 °C) and Class B (two isolates; active at -5 to -8 °C). We sequenced the 16S rRNA gene of 18 Class A INA isolates and identified 15 isolates as Enterobacteriaceae, while the remaining three as Pseudomonadaceae. The vast majority of our Class A INA isolates were likely Pantoea spp. with several isolates were deduced as either Pseudomonas, Cronobacter, and Klebsiella. We found that these 18 Class A INA isolates had acquired resistance to antibiotics erythromycin and ampicillin, which are considered two critically important antibiotics.

Conclusions

Our results showed that the prevalence of INA bacterial population varies across locations and seasons. Furthermore, our isolates were dominated by Class A and C INA bacteria. This study also cautions regarding the spread of antibiotic resistance among INA bacteria.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02521-1.

Successful Treatment of Pantoea agglomerans Bacteremia Using Oral Antibiotics

A 30-year-old female with a medical history of gastrointestinal reflux and intravenous methamphetamine use was admitted to the hospital with complaints of fever and chills. Pantoae agglomerans was isolated in one out of two blood cultures. Although information was limited about the duration and efficacy of oral antibiotics to treat this type of infection, the patient recovered with oral antibiotic treatment following a short course of intravenous antibiotics.

Gut microbiome alterations in hereditary angioedema

BACKGROUND

Hereditary angioedema (HAE) is a rare disease with wide intra- and interindividual clinical variation. There are no reliable indicators available in clinical practice to predict the onset and severity of HAE. Uncovering the changes in the gut microbiota in HAE patients may offer insight into a missing piece of the pathogenesis and help explain the clinical heterogeneity.

OBJECTIVE

Explore whether dysbiosis exists in patients with HAE and whether there are biomarkers to indicate the episodes.

METHODS

Fecal samples and clinical data were collected from patients with C1-inhibitor-related HAE and their healthy family members. Patients were grouped on the basis of the most recent conditions of HAE episodes and major clinical manifestations. The gut microbiota was evaluated by sequencing the 16S ribosomal RNA gene and analyzed for diversity.

RESULTS

Microbial richness and diversity were significantly reduced among patients who had recent HAE attacks, especially for those presenting with abdominal symptoms (P = .003 and P = .048 compared with healthy controls and patients with no recent episodes, respectively). Decreased Firmicutes and increased Proteobacteria were found among the individuals with a recent episode, along with a marked increase of pathogenic bacteria on the basis of the predictive functional profiling. Dysbiosis was restored after regular use of danazol or tranexamic acid. A combined biomarker composed of Bifidobacterium, Lachnospira, Paraprevotella, Desulfovibrio, and Staphylococcus was proposed to detect the recent edema episodes.

CONCLUSION

We reported alterations of the gut microbiome in patients with HAE and explored the possible role of bacteria in the etiology of edema episodes, which may provide new clues for the prediction of disease course, clinical treatment, and therapeutic evaluation.

Overview of paratransgenesis as a strategy to control pathogen transmission by insect vectors

This article presents an overview of paratransgenesis as a strategy to control pathogen transmission by insect vectors. It first briefly summarises some of the disease-causing pathogens vectored by insects and emphasises the need for innovative control methods to counter the threat of resistance by both the vector insect to pesticides and the pathogens to therapeutic drugs. Subsequently, the state of art of paratransgenesis is described, which is a particularly ingenious method currently under development in many important vector insects that could provide an additional powerful tool for use in integrated pest control programmes. The requirements and recent advances of the paratransgenesis technique are detailed and an overview is given of the microorganisms selected for genetic modification, the effector molecules to be expressed and the environmental spread of the transgenic bacteria into wild insect populations. The results of experimental models of paratransgenesis developed with triatomines, mosquitoes, sandflies and tsetse flies are analysed. Finally, the regulatory and safety rules to be satisfied for the successful environmental release of the genetically engineered organisms produced in paratransgenesis are considered.

Aerobic Commensal Conjunctival Microflora in Healthy Donkeys

Simple Summary

The mucosa of the conjunctival sac in mammals is colonized by a group of bacteria, and their interdependence is referred to as commensalism—the coexistence of two different species populations benefiting at least one of the partners. The presence of conjunctival bacterial commensal flora is very important for the capacity of the non-specific immune response. Some of the bacteria are described as conditionally pathogenic, meaning that in the case of breaking down protective barriers, they may act as pathogens. Knowledge of the commensal flora of healthy individuals is of great clinical importance in the diagnosis of pathological conditions. The aim of this study is to assess the presence and the composition of normal ocular microflora of healthy donkeys. To the best of the authors’ knowledge, this is the first report that provides knowledge about commensal microflora in the conjunctival sac of donkeys bred in Central Europe.

Abstract

From a clinical point of view, knowledge of the commensal microbial flora of the conjunctival sac in healthy individuals proves to be of great importance. The aim of this study was to assess the presence and the composition of normal ocular microflora of healthy donkeys. Fourteen clinically healthy donkeys (Equus asinus) participated in the study. After prior ophthalmological examination, which showed no abnormalities, a conjunctival swab was taken from each donkey from the right and left eye. Species-specific identification was based on a morphological assessment of bacterial colonies stained with the Gram technique, as well as on biochemical properties and the disk-diffusion method. Around 82% of samples were positive for bacteria cultivation; Pantoea agglomerans was the most prevalently detected species, followed by Moraxella lacunata. In conclusion, our study made it possible to determine the commensal flora of the conjunctival sac in donkeys. The obtained results also showed discrepancies in the composition of the conjunctival sac flora of donkeys and horses, despite the geographical proximity of performed studies. Knowledge of the commensal conjunctival flora of donkeys is of great clinical importance due to their greater exposure to corneal damage and infections than horses.

The Identification of Multidrug-Resistant Microorganisms including Bergeyella zoohelcum Acquired from the Skin/Prosthetic Interface of Amputees and Their Susceptibility to Medihoney™ and Garlic Extract (Allicin)

Users of prosthetic devices face the accumulation of potentially drug-resistant pathogenic bacteria on the skin/prosthesis interface. In this study, we took surface swabs of the skin/prosthesis interface of eleven disabled athletes to identify microorganisms present. In addition to determining their antimicrobial resistance profile, we assessed their sensitivity to Manuka honey and Garlic extract (allicin). Eleven volunteers were directed to swab the skin at the skin/prosthesis interface. After initial isolation of microorganisms, we employed the following general microbiological methods: Gram stain, Catalase test, Oxidase test, lactose fermenting capability, haemolytic capability, Staphaurex, mannitol fermenting capability, Streptex; API Staph, 20E, Candida, and BBL crystal identification system tests. Once identified, isolates were analysed for their sensitivity to penicillin, erythromycin, ampicillin, vancomycin, ceftazidime, ciprofloxacin, gentamicin, and colistin-sulphate. Isolates were also analysed for their sensitivity to allicin (Garlic Extract (GE)) and Manuka honey (Medihoney™) (MH). Eleven isolates were identified: Bacillus cereus, Staphylococcus haemolyticus, Staphylococcus aureus, Micrococcus luteus, Pseudomonas oryzihabitans, Micrococcus spp., Bacillus subtilis, Group D Streptococcus, Pantoea spp., Enterobacter cloacae, and Bergeyella zoohelcum. All isolates were resistant to 1 unit of penicillin and 10 μg of ampicillin. Bergeyella zoohelcum was observed to have the widest range of resistance with observed resistance against five of the eight antimicrobials employed in this study. This study highlights the prevalence of uncommon drug-resistant microorganisms on the skin within a vulnerable population, highlighting the potential for MH or GE intervention.

Timber-colonizing gram-negative bacteria as potential causative agents of respiratory diseases in woodworkers

Occurrence

Gram-negative bacteria occur commonly in the inner tissues of stored coniferous and deciduous timber, showing a marked variation in numbers. The greatest maximal numbers are found in the sapwood of coniferous timber. The common constituents of the Gram-negative biota are potentially pathogenic species of Enterobacteriaceae family of the genera Rahnella, Pantoea, Enterobacter, and Klebsiella. The air of wood-processing facilities is polluted with the wood-borne Gram-negative bacteria and produced by them endotoxin, as demonstrated worldwide by numerous studies.

Effects

There are three potential pathways of the pathogenic impact of wood-borne Gram-negative bacteria on exposed woodworkers: allergic, immunotoxic, and infectious. Allergic impact has been underestimated for a long time with relation to Gram-negative bacteria. Hopefully, the recent demonstration of the first documented case of hypersensitivity pneumonitis (HP) in woodworkers caused by Pantoea agglomerans which developed in extremely large quantities in birch sapwood, would speed up finding of new wood-related cases of HP caused by Gram-negative bacteria. The second pathway is associated with endotoxin, exerting strong immunotoxic (excessively immunostimulative) action. It has been demonstrated that endotoxin is released into wood dust in the form of nano-sized microvesicles, by peeling off the outer membrane of bacteria. Endotoxin microvesicles are easily inhaled by humans together with dust because of small dimensions and aerodynamic shape. Afterwards, they cause a nonspecific activation of lung macrophages, which release numerous inflammatory mediators causing an inflammatory lung reaction, chest tightness, fever, gas exchange disorders, and bronchospasm, without radiographic changes. The resulting disease is known as “Organic Dust Toxic Syndrome” or “toxic pneumonitis.” The potential third pathway of pathogenic impact is infection. The suspected species is Klebsiella pneumoniae that may occur commonly in wood dust; however, until now this pathway has not been confirmed.

Conclusion

Summarizing, Gram-negative bacteria-inhabiting timber should be considered, besides filamentous fungi and actinobacteria, as important risk factors of occupational disease in woodworkers that could be either HP with allergenic background or toxic pneumonitis elicited by endotoxin.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00420-021-01829-1.

A Thorn in a Haystack: A Rare Case of Septic Arthritis

Pantoea agglomerans is a facultative anaerobe and environmental bacterium that could be a cause of opportunistic human infections, especially in wound infection with plant material. Arthritis or synovitis secondary to penetrating plant thorn injuries is not frequently reported. We present the case of a 35-year-old otherwise healthy male with a bramble thorn penetrating injury of the left knee. P. agglomerans was isolated from the synovial fluid. The patient was treated with amoxicillin/clavulanate according to sensitivity testing. This case highlights the importance of precise and thorough medical history, especially for less common presentations, as well as source control.

Genomics-Informed Multiplex PCR Scheme for Rapid Identification of Rice-Associated Bacteria of the Genus Pantoea

The genus Pantoea forms a complex of more than 25 species, among which several cause diseases of various crop plants, including rice. Notably, strains of Pantoea ananatis and P. stewartii have been repeatedly reported to cause bacterial leaf blight of rice, whereas other authors have observed that P. agglomerans can also cause bacterial leaf blight of rice. The contribution of these and perhaps other species of Pantoea to plant diseases and yield losses of crop plants is currently not well documented, partly due to the lack of efficient diagnostic tools. Using 32 whole-genome sequences of the three major plant-pathogenic Pantoea spp., a set of PCR primers that detect each of the three species P. agglomerans, P. ananatis, and P. stewartii was designed. A multiplex PCR scheme which can distinguish these three species and also detects members of other Pantoea spp. was further developed. Upon validation on a set of reference strains, 607 suspected Pantoea strains that were isolated from rice leaves or seed originating from 11 African countries were screened. In total, 41 P. agglomerans strains from 8 countries, 79 P. ananatis strains from 9 countries, 269 P. stewartii strains from 9 countries, and 218 unresolved Pantoea strains from 10 countries were identified. The PCR protocol allowed detection of Pantoea bacteria grown in vitro, in planta, and in rice seed. The detection threshold was estimated as total genomic DNA at 0.5 ng/µl and heated cells at 1 × 10⁴ CFU/ml. This new molecular diagnostic tool will help to accurately diagnose major plant-pathogenic species of Pantoea. Due to its robustness, specificity, sensitivity, and cost efficiency, it will be very useful for plant protection services and for the epidemiological surveillance of these important crop-threatening bacteria.

Atypical pathogens associated with cardiac implantable electronic device infections

BACKGROUND

Cardiovascular implantable electronic device (CIED) infections are associated with significant morbidity and mortality making the identification of the causative organism critical. The vast majority of CIED infections are caused by Staphylococcal species. CIED infections associated with atypical pathogens are rare and have not been systematically investigated. The objective of this study is to characterize the clinical course, management and outcome in patients with CIED infection secondary to atypical pathogens.

METHODS

Medical records of all patients who underwent CIED system extraction at the University of Chicago Medical Center between January 2010 and November 2020 were retrospectively reviewed to identify patients with CIED infection. Demographic, clinical, infection-related and outcome data were collected. CIED infections were divided into typical and atypical groups based on the pathogens isolated.

RESULTS

Among 356 CIED extraction procedures, 130 (37%) were performed for CIED infection. Atypical pathogens were found in 5.4% (n = 7) and included Pantoea species (n = 2), Kocuria species (n = 1), Cutibacterium acnes (n = 1), Corynebacterium tuberculostearicum (n = 1), Corynebacterium striatum (n = 1), Stenotrophomonas maltophilia (n = 1), and Pseudozyma ahidis (n = 1). All patients with atypical CIED infections were successfully treated with total system removal and tailored antibiotic therapy. There were no infection-related deaths.

CONCLUSIONS

CIED infections with atypical pathogens were rare and associated with good outcome if diagnosed early and treated with total system removal and tailored antimicrobial therapy. Atypical pathogens cultured from blood, tissue or hardware in patients with CIED infection should be considered pathogens and not contaminants.

Pantoea Bacteriophage vB_PagS_MED16-A Siphovirus Containing a 2'-Deoxy-7-amido-7-deazaguanosine-Modified DNA

A novel siphovirus, vB_PagS_MED16 (MED16) was isolated in Lithuania using Pantoea agglomerans strain BSL for the phage propagation. The double-stranded DNA genome of MED16 (46,103 bp) contains 73 predicted open reading frames (ORFs) encoding proteins, but no tRNA. Our comparative sequence analysis revealed that 26 of these ORFs code for unique proteins that have no reliable identity when compared to database entries. Based on phylogenetic analysis, MED16 represents a new genus with siphovirus morphology. In total, 35 MED16 ORFs were given a putative functional annotation, including those coding for the proteins responsible for virion morphogenesis, phage-host interactions, and DNA metabolism. In addition, a gene encoding a preQ0 DNA deoxyribosyltransferase (DpdA) is present in the genome of MED16 and the LC-MS/MS analysis indicates 2'-deoxy-7-amido-7-deazaguanosine (dADG)-modified phage DNA, which, to our knowledge, has never been experimentally validated in genomes of Pantoea phages. Thus, the data presented in this study provide new information on Pantoea-infecting viruses and offer novel insights into the diversity of DNA modifications in bacteriophages.

Proteomics-based identification of orchid-associated bacteria colonizing the Epipactis albensis, E. helleborine and E. purpurata (Orchidaceae, Neottieae)

Using proteomics-based identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), we conducted the first analysis of the composition of endophytic bacteria isolated from different parts of selected Epipactis species, i.e. the buds, the inflorescences and the central part of the shoots, as well as the rhizomes. We identified aerobic and anaerobic bacteria, including such taxa as Bacillus spp., Clostridium spp., Pseudomonas spp. and Stenotrophomonas spp., which may be considered as promoting plant growth. Because most of the indicated bacteria genera belong to spore-producing taxa (spores allow bacterial symbionts to survive adverse conditions), we suggest that these bacteria species contribute to the adaptation of orchids to the environment. We found clear differences in the microbiome between investigated closely related taxa, i.e., Epipactis albensis, E. helleborine, E. purpurata and E. purpurata f. chlorophylla. Some of the analysed orchid species, i.e. E. albensis and E. purpurata co-occur in habitats, and their bacterial microbiomes differ from each other.

A Case of Nosocomial Outbreak of Pantoea agglomerans Related to Parenteral Nutrition Procedures

Pantoea agglomerans is a Gram-negative bacterium that infrequently infects humans. Most reports involving it are about infections in soft tissues or bone/joint infections caused by contamination from soil or penetrating trauma by vegetation, such as thorns and splinters. More frequently, it is found as an opportunistic pathogen in immunocompromised patients. It is not rare to find reports of bacteremia and sepsis from contamination of intravenous fluid, parenteral nutrition, blood products and anesthetic agents-that is, through contamination of medical devices and products. We reported a bacterial infection epidemic occurred in 2011 in a hospital in middle Italy which involved different hospital wards; Pantoea agglomerans was isolated from blood cultures of all infected patients and the source of infection was identified in contaminated parenteral nutrition prepared from the local pharmacy.