Eggshell and environmental bacteria contribute to the intestinal microbiota of growing chickens

Background: The initial intestinal microbiota acquired from different sources has profound impacts on animal health and productivity. In modern poultry production practices, the source(s) of the establishing microbes and their overall contribution during development of gastrointestinal tract communities are still unclear. Using fertilized eggs from two independent sources, we assessed the impact of eggshell-and environmental-associated microbial communities on the successional processes and bacterial community structure throughout the intestinal tract of chickens for up to 6 weeks post-hatch.Results: Culturing and sequencing techniques identified a viable, highly diverse population of anaerobic bacteria on the eggshell. The jejunal, ileal, and cecal microbial communities for the egg-only, environment-only, and conventionally raised birds generally displayed similar successional patterns characterized by increasing community richness and evenness over time, with strains of Enterococcus, Romboutsia, and unclassified Lachnospiraceae abundant for all three input groups in both trials. Bacterial community structures differed significantly based on trial and microbiota input with the exception of the egg-exposed and conventional birds in the jejunum at week 1 and the ileum at week 6. Cecal community structures were different based on trial and microbiota input source, and cecal short-chain fatty acid profiles at week 6 highlighted functional differences as well.Conclusion: We identified distinct intestinal microbial communities and differing cecal short-chain fatty acid profiles between birds exposed to the microbiota associated with either the eggshell or environment, and those of conventionally hatched birds. Our data suggest the eggshell plays an appreciable role in the development of the chicken intestinal microbiota, especially in the jejunum and ileum where the community structure of the eggshellonly birds was similar to the structure of conventionally hatched birds. Our data identify a complex interplay between the eggshell and environmental microbiota during establishment and succession within the chicken gut.Further studies should explore the ability of eggshell-and environment-derived microbes to shape the dynamics of succession and how these communities can be targeted through interventions to promote gut health and mitigate food-borne pathogen colonization in poultry.

Isolation and Antibiotic-Resistant Pattern of Opportunistic Infectious Microbes from the Infected Sites of Oral Cancer Patients Compared to That of Healthy People Oral Microbiota

Introduction: Oral cancer is the third most prominent type of cancer in Bangladesh. During or after oral cancer treatment, immune-compromised cancer patients may be susceptible to an infection by multi-drug-resistant opportunistic microbes. This study aims to identify the prevalent microorganisms from the infected site of oral cancer patients and observe their antibiotic susceptibility pattern. Materials and Methods: Clinical samples were collected from the infected sites of oral cancer patients and healthy people. The swabs collected were placed on nutrient agar slant, then incubated for 24 hours at 37ºC. Bacteria from the slant were inoculated in several selective media (Mannitol Salt Agar Media, KF Streptococcus Agar media, Cetrimide Agar, Eosin Methylene Blue Agar). Several biochemical tests identified opportunistic microorganisms. Finally, the antibiotic susceptibility test was performed by the Kirby Bauer disc diffusion method. Results: The study found that 65.4% of microbes isolated from the patients’ oral cavities were Gram-negative bacteria, and 34.6% were Gram-positive bacteria. Among the patient group isolates (n = 55), the most prevalent organism was Pseudomonas spp. (30;54.54%). Others were Klebsiella spp. (27;49.09%), Staphylococcus spp. (24;43.63%), E. coli (14;25.45%), Streptococcus spp. (14;25.45%), Proteus spp. (12;21.8%) and Enterococcus spp. (6;10.90%). Both Gram-positive and Gram-negative microbes from the patient group have shown high resistance to the commonly used antibiotics. In the control group (n = 50), the most prevalent organism was Staphylococcus spp. (15;30%). Other organisms were Streptococcus spp. (6;12%), Klebsiella spp. (11;22%), E. coli (3;6%), Streptococcus spp. (14;25.45%), Pseudomonas spp. (8;16%). The microbes of the control group showed less resistance to the antibiotics and rather showed sensitivity to them. Conclusion: The study revealed a high prevalence of multi-drug-resistant opportunistic microbes on immune-compromised oral cancer patients compared to microbes isolated from healthy people’s oral cavity.

A Prospective Study on the Efficiency of Ciprofloxacin in Combination with Chloramphenicol against Multiple Antibiotics Resistant <i>Klebsiella pneumonia</i>

Pneumonia is the single largest infectious cause of death in children worldwide and also a form of an acute respiratory infection that affects the lung. The purpose of the study was to develop a new approach to treat antibiotic-resistant K. pneumoniae infection. This study aimed in quest of a drug to combine with ciprofloxacin, a broad spectrum antibiotic frequently used to treat lung infections. Methodology: A total of 23 lung infection bacterial samples were collected and studied against 14 antibiotics of different classes. The disk diffusion method was performed to determine synergy screening, MIC value, and qualitative toxicity analysis of ciprofloxacin and chloramphenicol combination. Results: After primary screening of antibiotic susceptibility, they were categorized into multidrug-resistant (MDR), extensively drug-resistant (XDR) and pan drug-resistant (PDR) pathogens where 9 isolates were MDR, 5 were XDR and 3 isolates were PDR. Furthermore, they were trialed in combination ciprofloxacin along with other 7 drugs in disk diffusion to explore the synergistic effect. The combination of ciprofloxacin and moxifloxacin, ciprofloxacin and chloramphenicol were found to be synergic. Then the MIC test was done for the combination ciprofloxacin and chloramphenicol. When the MIC result was generated, the MIC of the respective combination was analyzed. Furthermore, the fractional inhibitory concentration (FIC) was calculated and in accordance with the results of the FIC index, ciprofloxacin-chloramphenicol combination has shown value 0.4510 which revealed a synergistic effect against multi-drug resistant Klebsiella pneumoniae. Conclusion: Given these points, if the efficiency of this antibiotic can be accelerated from combination with other drugs, it might be lifesaving and cost effective as well.

A Study of Prevalence and Pathogenic Activity of Bacteria in the Air of Dhaka City and Their Antimicrobial Resistance Pattern

Bangladesh composes the most polluted air with Dhaka securing the top position. The purpose of the study is the enumeration of the prevalence of pathogenic bacteria in Dhaka city’s air and their antibiotic susceptibility to the common antibiotics. For the sample collection, different selective media was exposed in air where the highest and lowest CFU was 137 and 1 respectively. Pathogens were screened through Hemolysis, DNase and Coagulase test and identified by 16s rRNA sequencing followed by antibiotic susceptibility test. 16s rRNA sequencing revealed that the organisms were Bacillus altitudinis strain 41KF2bT.28, Bacillus licheniformis strain QMA46-2, Bacillus altitudinis, Bacillus pumilis strain BJ-DEBCR-34, Staphylococcus aureus strain TPS3156, Bacillus sp CO16, Pseudomonas sp strain 96LC22 and Shigella dysenteriae strain ATCC 13313. Shigella dysenteriae, Staphylococcus aureus were 81.81% and 54.54% resistant to the antibiotics. Whole-genome sequencing would help to observe mutations in the traits as changes in hemolytic activity were found during pathogenecity tests.

Two distinct subpopulations of marginal zone B cells exhibit differential antibody-producing capacities and radioresistance

Marginal zone(MZ)B cells,which are splenic innate-like B cells that rapidly secrete antibodies(Abs)against blood-borne pathogens,are composed of heterogeneous subpopulations.Here,we showed that MZ B cells can be divided into two distinct subpopulations according to their CD80 expression levels.CD80^(high)MZ B cells exhibited greater Ab-producing,proliferative,and IL-10-secreting capacities than did CD80^(low)MZ B cells.Notably,CD80^(high)MZ B cells survived 2-Gy whole-body irradiation,whereas CD80^(low)MZ B cells were depleted by irradiation and then repleted with one month after irradiation.Depletion of CD80^(low)MZ B cells led to accelerated development of type II collagen(CII)-induced arthritis upon immunization with bovine CII.CD80^(high)MZ B cells exhibited higher expression of genes involved in proliferation,plasma cell differentiation,and the antioxidant response.CD80^(high)MZ B cells expressed more autoreactive B cell receptors(BCRs)that recognized double-stranded DNA or CII,expressed more immunoglobulin heavy chain sequences with shorter complementarity-determining region 3 sequences,and included more clonotypes with no N-nucleotides or with B-1a BCR sequences than CD80^(low)MZ B cells.Adoptive transfer experiments showed that CD21^(+)CD23^(+)transitional 2 MZ precursors preferentially generated CD80^(low)MZ B cells and that a proportion of CD80^(low)MZ B cells were converted into CD80^(high)MZ B cells;in contrast,CD80^(high)MZ B cells stably remained CD80^(high)MZ B cells.In summary,MZ B cells can be divided into two subpopulations according to their CD80 expression levels,Ab-producing capacity,radioresistance,and autoreactivity,and these findings may suggest a hierarchical composition of MZ B cells with differential stability and BCR specificity.

Rational design of oral drugs targeting mucosa delivery with gut organoid platforms

Effective oral drugs and vaccines require high delivery efficiency across the gastrointestinal epithelia and protection of medically effective payloads(i.e.,immunogens)against gastric damage.In this study,hollowed nanocarriers(NCs:silica nanospheres and gold nanocages)with poly-l-lysine(PLL)coating and mammalian orthoreovirus cell attachment proteinσ1 functionalization(NC-PLL-σ1)were explored as functional oral drug delivery vehicles(ODDVs).The transport of these ODDVs to mucosal lymphoid tissues could be facilitated by microfold cells(M-cells)mediated transcytosis(viaσ1-α2–3-linked sialic acids adherence)across gastrointestinal epithelia.PLL coating provided protection and slow-release of rhodamine 6 G(R6G),a model payload.The transport effectiveness of these ODDVs was tested on intestinal organoid monolayers in vitro.When compared with other experimental groups,the fully functionalized ODDV system(with PLL-σ1)demonstrated two significant advantages:a significantly higher transport efficiency(198%over blank control at 48 h);and protection of payloads which led to both better transport efficiency and extended-release of payloads(61%over uncoated carriers at 48 h).In addition,it was shown that the M cell presence in intestinal organoid monolayers(modulated by Rank L stimulation)was a determining factor on the transport efficiency of the ODDVs:more M-cells(induced by higher Rank L)in the organoid monolayers led to higher transport efficiency for ODDV-delivered model payload(R6G).The fully functionalized ODDVs showed great potential as effective oral delivery vehicles for drugs and vaccines.

Calreticulin surface presentation: a signal for natural killer cells to attack

In a recent article published in Nature,Sen Santara et al.report a general mechanism that allows endoplasmic reticulum(ER)stress,a common response to many cellular dysfunctions,to signal to natural killer(NK)cells to destroy the stressed cell(Fig.1).1 This mechanism suggests that targeting this signaling pathway might serve as a common therapeutic approach to treat disparate diseases,including cancers and infections.The innate immune system recognizes molecular signa-tures that indicate threats to the organism,and transduces these signatures into an immune response to counter these threats.As part of the innate immune system,NK cells constitute a lymphoid immune cell type that kills infected or cancerous cells on the basis of their presentation of specific ligands or markers on the surface of abnormal cells.

Notch signaling and its emerging role in autoimmunity

Studies of notch signaling in immune cells have uncovered critical roles for this pathway both during the differentiation and effector function phases of immune responses. Cells of the myeloid lineage, including macrophages and dendritic cells, function as key components of innate immune defense against infection and, by acting as antigen presenting cells, can instruct cells of the adaptive immune response, specifically CD4 and CD8 T cells. Tight regulation of this functional interaction is needed to ensure a well-balanced immune response and its dysregulation may indirectly or directly cause the tissue damage characteristic of autoimmune diseases. In this review, the focus will be placed on those recent findings which support a role for notch signaling in inflammatory responses mediated by macrophages and other myeloid lineage cells, as well as peripheral T cells, and their relevance to inflammatory and autoimmne diseases.

The numbers of fungi:are the most speciose genera truly diverse?

Fungi play vital roles in ecosystems as endophytes,pathogens and saprobes.The current estimate of fungal diversity is highly uncertain,ranging from 1.5 to 12 million,but only around 150,000 species have been named and classified to date.Since the introduction of DNA based methods for species identification,the number of newly described taxa has increased from approximately 1000 to around 2000 yearly.This demonstrates the importance of DNA based methods to identify and distin-guish species,especially cryptic species.Many novel species from recent studies have been found in historically understudied regions and habitats,but these still represent only a small percentage of the estimated species.In this paper,we examine 16 genera from the top 40 most speciose genera as listed in Species Fungorum as case studies to examine the diversity of taxa in each genus.The genera treated herein are Cercospora,Diaporthe,Meliola,Passalora,Phyllachora,Phyllosticta,Pseudocer-cospora,Ramularia(ascomycetes)and Cortinarius,Entoloma,Inocybe,Marasmius,Psathyrella,Puccinia,Russula,Uromyces(basidiomycetes).We critically evaluate the number of species in these genera and correlate these numbers with the number of entries in GenBank.We introduce 18 new species Apiospora multiloculata,Candolleomyces thailandensis,Cortinarius acutoproximus,Cortinarius melleoalbus,Cortinarius pacificus,Cortinarius parvoacetosus,Diaporthe guizhouensis,Entoloma pseudosubcorvinum,Inocybe meirensongia,Marasmius albulus,Marasmius obscuroaurantiacus,Meliola camporesii,Phyl-lachora siamensis,Phyllosticta doitungensis,Picipes yuxiensis,Pseudocercospora vignae,Puccinia maureanui and Russula inornata.We also introduce a new record of Candolleomyces cladii-marisci and Inocybe iringolkavensis.We discuss the genera Colletotrichum and Pleurotus that are speciose,but do not occur in the top 40.We hypothesize whether there might be more species in these genera and discuss why these genera have some of the largest number of species.

Fungal diversity notes 1512–1610: taxonomic and phylogenetic contributions on genera and species of fungal taxa

This article is the 14th in the Fungal Diversity Notes series,wherein we report 98 taxa distributed in two phyla,seven classes,26 orders and 50 families which are described and illustrated.Taxa in this study were collected from Australia,Brazil,Burkina Faso,Chile,China,Cyprus,Egypt,France,French Guiana,India,Indonesia,Italy,Laos,Mexico,Russia,Sri Lanka,Thailand,and Vietnam.There are 59 new taxa,39 new hosts and new geographical distributions with one new combination.The 59 new species comprise Angustimassarina kunmingense,Asterina lopi,Asterina brigadeirensis,Bartalinia bidenticola,Bartalinia caryotae,Buellia pruinocalcarea,Coltricia insularis,Colletotrichum fexuosum,Colletotrichum thasutense,Coniochaeta caraganae,Coniothyrium yuccicola,Dematipyriforma aquatic,Dematipyriforma globispora,Dematipyriforma nilotica,Distoseptispora bambusicola,Fulvifomes jawadhuvensis,Fulvifomes malaiyanurensis,Fulvifomes thiruvannamalaiensis,Fusarium purpurea,Gerronema atrovirens,Gerronema favum,Gerronema keralense,Gerronema kuruvense,Grammothele taiwanensis,Hongkongmyces changchunensis,Hypoxylon inaequale,Kirschsteiniothelia acutisporum,Kirschsteiniothelia crustaceum,Kirschsteiniothelia extensum,Kirschsteiniothelia septemseptatum,Kirschsteiniothelia spatiosum,Lecanora immersocalcarea,Lepiota subthailandica,Lindgomyces guizhouensis,Marthe asmius pallidoaurantiacus,Marasmius tangerinus,Neovaginatispora mangiferae,Pararamichloridium aquisubtropicum,Pestalotiopsis piraubensis,Phacidium chinaum,Phaeoisaria goiasensis,Phaeoseptum thailandicum,Pleurothecium aquisubtropicum,Pseudocercospora vernoniae,Pyrenophora verruculosa,Rhachomyces cruralis,Rhachomyces hyperommae,Rhachomyces magrinii,Rhachomyces platyprosophi,Rhizomarasmius cunninghamietorum,Skeletocutis cangshanensis,Skeletocutis subchrysella,Sporisorium anadelphiae-leptocomae,Tetraploa dashaoensis,Tomentella exiguelata,Tomentella fuscoaraneosa,Tricholomopsis lechatii,Vaginatispora favispora and Wetmoreana blastidiocalcarea.The new combination is Torula sundara.The 39 new records on hosts and geographical distribution comprise Apiospora guiyangensis,Aplosporella artocarpi,Ascochyta medicaginicola,Astrocystis bambusicola,Athelia rolfsii,Bambusicola bambusae,Bipolaris luttrellii,Botryosphaeria dothidea,Chlorophyllum squamulosum,Colletotrichum aeschynomenes,Colletotrichum pandanicola,Coprinopsis cinerea,Corylicola italica,Curvularia alcornii,Curvularia senegalensis,Diaporthe foeniculina,Diaporthe longicolla,Diaporthe phaseolorum,Diatrypella quercina,Fusarium brachygibbosum,Helicoma aquaticum,Lepiota metulispora,Lepiota pongduadensis,Lepiota subvenenata,Melanconiella meridionalis,Monotosporella erecta,Nodulosphaeria digitalis,Palmiascoma gregariascomum,Periconia byssoides,Periconia cortaderiae,Pleopunctum ellipsoideum,Psilocybe keralensis,Scedosporium apiospermum,Scedosporium dehoogii,Scedosporium marina,Spegazzinia deightonii,Torula fci,Wiesneriomyces laurinus and Xylaria venosula.All these taxa are supported by morphological and multigene phylogenetic analyses.This article allows the researchers to publish fungal collections which areimportant for future studies.An updated,accurate and timely report of fungus-host and fungus-geography is important.We also provide an updated list of fungal taxa published in the previous fungal diversity notes.In this list,erroneous taxa and synonyms are marked and corrected accordingly.

Notes for genera:Ascomycota

Knowledge of the relationships and thus the classification of fungi,has developed rapidly with increasingly widespread use of molecular techniques,over the past 10–15 years,and continues to accelerate.Several genera have been found to be polyphyletic,and their generic concepts have subsequently been emended.New names have thus been introduced for species which are phylogenetically distinct from the type species of particular genera.The ending of the separate naming of morphs of the same species in 2011,has also caused changes in fungal generic names.In order to facilitate access to all important changes,it was desirable to compile these in a single document.The present article provides a list of generic names of Ascomycota(approximately 6500 accepted names published to the end of 2016),including those which are lichen-forming.Notes and summaries of the changes since the last edition of‘Ainsworth&Bisby’s Dictionary of the Fungi’in 2008 are provided.The notes include the number of accepted species,classification,type species(with location of the type material),culture availability,life-styles,distribution,and selected publications that have appeared since 2008.This work is intended to provide the foundation for updating the ascomycete component of the"Without prejudice list of generic names of Fungi"published in 2013,which will be developed into a list of protected generic names.This will be subjected to the XIXth International Botanical Congress in Shenzhen in July 2017 agreeing to a modification in the rules relating to protected lists,and scrutiny by procedures determined by the Nomenclature Committee for Fungi(NCF).The previously invalidly published generic names Barriopsis,Collophora(as Collophorina),Cryomyces,Dematiopleospora,Heterospora(as Heterosporicola),Lithophila,Palmomyces(as Palmaria)and Saxomyces are validated,as are two previously invalid family names,Bartaliniaceae and Wiesneriomycetaceae.Four species of Lalaria,which were invalidly published are transferred to Taphrina and validated as new combinations.Catenomycopsis Tibell&Constant.is reduced under Chaenothecopsis Vain.,while Dichomera Cooke is reduced under Botryosphaeria Ces.&De Not.(Art.59).