Development of indigestible IgA antibody for restoring microbiome balance

Dysbiosis, especially in the gut plays a crucial role in the pathogenesis of a wide variety of diseases, including inflammatory bowel disease, colorectal cancer, cardiovascular disease, obesity, diabetes and multiple sclerosis. At mucosal surfaces, mucosal polymeric immunoglobulin A（IgA）antibodies are known to be important to regulate the gut microbiota as well as to exclude infection induced by pathogenic bacteria or virus such as influenza and SARS-CoV-2（severe acute respiratory syndrome coronavirus 2）. Since the 1970s, oral administration of IgA or IgG antibodies has been performed against infectious enteritis caused by pathogenic Escherichia coli or Clostridioides difficile. However, none of them has been successfully developed as an antibody drug up to now. Although IgA is well known to modulate the gut commensal microbiota, the therapeutic IgA drugs to treat dysbiosis has not been developed. Here, we discuss the advantages of therapeutic IgA antibodies.Alternate :抄録Dysbiosisは、健康な微生物叢と比較した微生物組成の変化であり、腸内微生物多様性の減少および微生物分類群の変化を特徴とする。腸内のdysbiosisはまた、炎症性腸疾患、結腸直腸がん、心血管疾患、肥満、糖尿病および多発性硬化症を含むさまざまな疾患の病因において重要な役割を果たすと提唱されている。腸の多量体免疫グロブリンA（IgA）抗体は、腸内微生物叢を調節するだけではなく、病原性細菌、インフルエンザやSARS-CoV-2（重症急性呼吸器症候群コロナウイルス2）などのウイルス感染を粘膜部位から排除するのに重要であることが、多くのエビデンスから示されている。1970年代以降、治療用IgAまたはIgGの経口投与試験が、主に病原性大腸菌またはディフィシル菌によって引き起こされる感染性腸炎を治療するために行われてきた。しかし、現在まで臨床応用として開発に成功したものはない。腸内病原体に対する防御機能に加えて、IgAは腸内共生微生物叢を調節して共生に導くことがよく知られているが、dysbiosisを治療するためのIgA治療薬の開発も進んでいない。本稿では、治療用IgA抗体の利点とその開発について議論する。

Research Dynamics within a New Multi-Institutional Cross-Disciplinary Translational Team (MCTT): A Formative Study

OBJECTIVES/GOALS: This report evaluates participants'experiences from three universities who assembled a complex grant proposal related to research on post-acute sequala of COVID-19 (PASC), also called long COVID. Activities reviewed ranged from the assembly of the team to responses to reviews by the National Center for Advancing Translational Sciences (NCATS). METHODS/STUDY POPULATION: Data were collected by means of semi-structured interviews, conducted and recorded on Zoom, with a sample of 15 scientists and staff both during proposal assembly and following proposal review. The sample comprised 40% of the total team equally selected from the 3 universities, The interview protocol was reviewed by the IRB at UTMB and the interviews were recorded on Zoom, and analyzed by means of the constant comparative strategy in the grounded theory method of qualitative research. Given the relatively small number of interviews in this project, we paid special attention to preserving the confidentiality of respondents. Only the verbal tracks of the interviews were professionally transcribed. Respondents were asked to suggest changes for future inter-organizational proposals. RESULTS/ANTICIPATED RESULTS: FIRST INTERVIEWS *LEADERSHIP: The scope of leadership opportunities was expanded as sub-teams in specific areas such as community engagement were formed. *TEAM: Each university's community engagement team specializes in a different ethnic clientele, precluding a singular statement for the proposal. SECOND INTERVIEWS *LEADERSHIP: Staff members noted that the team concept too easily evolved into a bureaucratic format, resulting in less negotiation and more direction. *ASSEMBLY TASKS: The Writing Team turned out to be one of the most critical staff teams. *COMMUNICATION: The behavioral scientists in community engagement do not necessarily share paradigms (e.g., public health, psychology, and social work). They had difficulty generating productive communication and a unified statement for the proposal. DISCUSSION/SIGNIFICANCE: The scientists, as a group, suggested that future proposals should focus on one general topic, such as the microbiome, as opposed to attempting to integrate widely divergent interests. The scientists as a group should decide a priori whether to treat innovative ideas such as machine learning science as a science or a service.

Resetting urban human-microbial relations in pandemic times

Microbes, particularly of the viral kind, are currently preoccupying human activity and concerns due to the COVID-19 pandemic. Although for a long time there has been fear associated with ‘germs', notably viruses and bacteria and the diseases they cause, the pandemic has set these fears into overdrive. As serious as this ongoing event is, there are broader interests and important alternative narratives about the microbial world permeating current thinking, based on research that intersects with and includes biopolitical and relational research in geography. In an attempt at balancing the prevailingly negative discourses about microbes and the potential harms they can cause, and to encourage more geographers to contribute to understanding human-microbial relations, this paper draws together recent research across disciplines to discuss the prevalence and role of microbes in environments and in and on human bodies. Drawing on ideas of more-than-human care, the paper shows how geographers and other social scientists can and are already helping reset human-microbial relations, and where further work can productively be done. © 2023 The Authors. Geography Compass published by John Wiley & Sons Ltd.

Dispersal of bacteria and stimulation of permafrost decomposition by Collembola

Contrary to most soils, permafrost soils have the atypical feature of being almost entirely deprived of soil fauna. Abiotic constraints on the fate of permafrost carbon after thawing are increasingly understood, but biotic constraints remain scarcely investigated. Incubation studies, essential to estimate effects of permafrost thaw on carbon cycling, typically measure the consequences of permafrost thaw in isolation from the topsoil and thus do not account for the effects of altered biotic interactions because of e.g. colonization by soil fauna. Microarthropods facilitate the dispersal of microorganisms in soil, both on their cuticle (ectozoochory) and through their digestive tract (endozoochory), which may be particularly important in permafrost soils, considering that microbial community composition can strongly constrain permafrost biogeochemical processes.Here we tested how a model species of microarthropod (the CollembolaFolsomia candida) affected aerobic CO2 production of permafrost soil over a 25 d incubation. By using Collembola stock cultures grown on permafrost soil or on an arctic topsoil, we aimed to assess the potential for endo- and ectozoochory of soil bacteria, while cultures grown on gypsum and sprayed with soil suspensions would allow the observation of only ectozoochory.The presence of Collembola introduced bacterial amplicon sequence variants (ASVs) absent in the no-Collembola control, regardless of their microbiome manipulation, when considering presence–absence metrics (unweighted UniFrac metrics), which resulted in increased species richness. However, these introduced ASVs did not induce changes in bacterial community composition as a whole (accounting for relative abundances, weighted UniFrac), which might only become detectable in the longer term.CO2 production was increased by 25.85 % in the presence of Collembola, about half of which could be attributed to Collembola respiration based on respiration rates measured in the absence of soil. We argue that the rest of the CO2 being respired can be considered a priming effect of the presence of Collembola, i.e. a stimulation of permafrost CO2 production in the presence of active microarthropod decomposers. Overall, our findings underline the importance of biotic interactions in permafrost biogeochemical processes and the need to explore the additive or interactive effects of other soil food web groups of which permafrost soils are deprived.

The potential use of probiotics in alleviating psychological symptoms of long covid-19

IDDF2022-ABS-0207 Figure 1ConclusionsA potential connection exists between the psychiatric sequelae of COVID-19 and the gut microbiome. These findings also provide insights on probiotics as a potential adjunctive treatment to conventional psychotropic medications in alleviating psychiatric sequelae post COVID-19.

Apitherapy and Periodontal Disease: Insights into In Vitro, In Vivo, and Clinical Studies

Periodontal diseases are caused mainly by inflammation of the gums and bones surrounding the teeth or by dysbiosis of the oral microbiome, and the Global Burden of Disease study (2019) reported that periodontal disease affects 20–50% of the global population. In recent years, more preference has been given to natural therapies compared to synthetic drugs in the treatment of periodontal disease, and several oral care products, such as toothpaste, mouthwash, and dentifrices, have been developed comprising honeybee products, such as propolis, honey, royal jelly, and purified bee venom. In this study, we systematically reviewed the literature on the treatment of periodontitis using honeybee products. A literature search was performed using various databases, including PubMed, Web of Science, ScienceDirect, Scopus, clinicaltrials.gov, and Google Scholar. A total of 31 studies were reviewed using eligibility criteria published between January 2016 and December 2021. In vitro, in vivo, and clinical studies (randomized clinical trials) were included. Based on the results of these studies, honeybee products, such as propolis and purified bee venom, were concluded to be effective and safe for use in the treatment of periodontitis mainly due to their antimicrobial and anti-inflammatory activities. However, to obtain reliable results from randomized clinical trials assessing the effectiveness of honeybee products in periodontal treatment with long-term follow-up, a broader sample size and assessment of various clinical parameters are needed.

Obstructive Sleep Apnea as a Risk Factor for COVID-19 Severity—The Gut Microbiome as a Common Player Mediating Systemic Inflammation via Gut Barrier Dysfunction

The novel corona virus that is now known as (SARS-CoV-2) has killed more than six million people worldwide. The disease presentation varies from mild respiratory symptoms to acute respiratory distress syndrome and ultimately death. Several risk factors have been shown to worsen the severity of COVID-19 outcomes (such as age, hypertension, diabetes mellitus, and obesity). Since many of these risk factors are known to be influenced by obstructive sleep apnea, this raises the possibility that OSA might be an independent risk factor for COVID-19 severity. A shift in the gut microbiota has been proposed to contribute to outcomes in both COVID-19 and OSA. To further evaluate the potential triangular interrelationships between these three elements, we conducted a thorough literature review attempting to elucidate these interactions. From this review, it is concluded that OSA may be a risk factor for worse COVID-19 clinical outcomes, and the shifts in gut microbiota associated with both COVID-19 and OSA may mediate processes leading to bacterial translocation via a defective gut barrier which can then foster systemic inflammation. Thus, targeting biomarkers of intestinal tight junction dysfunction in conjunction with restoring gut dysbiosis may provide novel avenues for both risk detection and adjuvant therapy.

OBEMIRISK‐Knowledge platform for assessing the risk of bisphenols on gut microbiota and its role in obesogenic phenotype: looking for biomarkers

“Obemirisk – Knowledge platform for assessing the risk of Bisphenols on gut microbiota and its role in obesogenic phenotype: looking for biomarkers” was a knowledge transfer project funded by the European Food Safety Authority (EFSA) that integrated a multidisciplinary team from Spain, France, Belgium, Slovakia and Poland. This project aimed to strengthen the knowledge capacity to assess the risk of bisphenol A and several structural analogues on gut microbiota that could mediate the obesogenic phenotype in childhood. Protocols and methodologies from different fields such as chemical analysis (food and biosamples), nutrition (surveys and questionnaires), microbiology (culturomics and metagenomics), and gene reporter assay (AhR‐Ligand) have been applied and shared. Several data generated under the project are available under open publications and databases for the Consortium and scientific community. Common documents and publications integrating data from endocrine disrupting chemicals (EDCs), bisphenols, microbiota dysbiosis and obesity were elaborated. A networking and specific capacity‐building programmes have been implemented to produce and share the new data on bisphenols data food composition, microbiota and its impact on obesity between providers and recipients’ partners. Scientific exchanges and specific designed courses provided training for students in the risk characterization related domains. The project was mainly focused on the bisphenols´ presence in consumed foods by Spanish children and in several children biosamples (saliva, urine, nails, and hair). Moreover, a pilot project on obese vs. normal‐weight children allowed to determine the obesity‐linked microbiota dysbiosis through metagenomics and specific biomarkers of the dysregulated microbiota‐immune system axis (AhR‐Ligands). The Obemirisk project applied a collaborative and multidisciplinary approach to establish scientific data compilation for harmonising risk assessment and to perform trainings on next generation of risk assessment where microbiome disruption might become a robust biomarker to be used in food safety. Several aspects of the process of capacity building have been mainly conceptual due to the COVId‐19 pandemic and will be further implemented through presential exchanges. Moreover, the consortium work strategy can also propose further EU collaborations for refining and elucidating the impact and mechanisms of bisphenols altering human microbiomes and triggering obesity. The knowledge, analyses and the integrative approach will be extrapolated for other foods, age ranges, geographical areas, and other biomatrices.For grant agreements: © OBEMIRISK consortium, 2022

Quantitative Efficacy of Common Virucidal Disinfectants Against Viral Surrogates on Porous and Nonporous Surfaces

The objectives of this effort were threefold: (a) compare Ebola virus (EBOV) with a potential surrogate, the enveloped vaccinia virus (VACV), for susceptibility to disinfectants;(b) generate efficacy data for five U.S. Environmental Protection Agency-registered virucidal chemicals and one experimental disinfectant, 5 percent vinegar, against VACV;and (c) compare the efficacy of three chemicals against Phi 6 (a bacteriophage surrogate for EBOV) and VACV. The Organisation for Economic Co-operation and Development (OECD) method was adopted for efficacy evaluations. Of the three test viruses, VACV was found be the most persistent virus. Of six disinfectants, Peridox disinfectant (Contec;Spartanburg, SC) was most effective against all three viruses. Bioxy-S sanitizer (Atomes, Inc.;Quebec, Canada) was effective against all three viruses. The other four disinfectants were not very effective against VACV. Peridox disinfectant, 0.2 percent peracetic acid (PAA), and 0.5 percent bleach were effective against Phi 6 in the absence of blood. In the presence of blood (dried and wet), both Peridox disinfectant and PAA were equally effective against Phi 6. VACV is recommended as a potential surrogate for EBOV. More importantly, this study highlights that the DoD must generate its own database on efficacy of disinfectants for military surfaces to select effective chemicals in the event of a pandemic resulting from an infectious virus.

Effects of Selenium Supplementation on Rumen Microbiota, Rumen Fermentation, and Apparent Nutrient Digestibility of Ruminant Animals: A Review

Enzymes excreted by rumen microbiome facilitate the conversion of ingested plant materials into major nutrients (e.g., volatile fatty acids (VFA) and microbial proteins) required for animal growth. Diet, animal age, and health affect the structure of the rumen microbial community. Pathogenic organisms in the rumen negatively affect fermentation processes in favor of energy loss and animal deprivation of nutrients in ingested feed. Drawing from the ban on antibiotic use during the last decade, the livestock industry has been focused on increasing rumen microbial nutrient supply to ruminants through the use of natural supplements that are capable of promoting the activity of beneficial rumen microflora. Selenium (Se) is a trace mineral commonly used as a supplement to regulate animal metabolism. However, a clear understanding of its effects on rumen microbial composition and rumen fermentation is not available. This review summarized the available literature for the effects of Se on specific rumen microorganisms along with consequences for rumen fermentation and digestibility. Some positive effects on total VFA, the molar proportion of propionate, acetate to propionate ratio, ruminal NH3-N, pH, enzymatic activity, ruminal microbiome composition, and digestibility were recorded. Because Se nanoparticles (SeNPs) were more effective than other forms of Se, more studies are needed to compare the effectiveness of synthetic SeNPs and lactic acid bacteria enriched with sodium selenite as a biological source of SeNPs and probiotics. Future studies also need to evaluate the effect of dietary Se on methane emissions.

IS IT POSSIBLE TO PREDICT VENTILATOR ASSOCIATED PNEUMONIA ETIOLOGY IN COVID-19 PATIENTS?

COVID-19 infection is no exception and may predispose to secondary bacterial and/or fungal co-infections like COVID-19 Associated Pulmonary Aspergillosis resulting in poor clinical outcomes especially among critically ill patients who require mechanical ventilation. Paolo Gaibani et al. conducted a prospective study (April to May, 2020) in a tertiary hospital in Bologna, Italy to assess the profile of the lower respiratory tract microbiome of critically ill patients with COVID-19 as compared to COVID-19 negative patients by using a 16S rRNA profiling on bronchoalveolar lavage samples. The dysbiosis observed in critically ill patients with COVID-19 was therefore characterized by the reduction of commensal bacterial species and predominance of opportunistic gram-negative pathogens frequently associated with multidrug resistance.

An investigation into the presence of pathogens on inanimate surfaces in the hospital environment

BackgroundThe hospital environment is understood to play an important role in the transmission of nosocomial pathogens, with inanimate surfaces facilitating pathogen movement and persistence in the environment. The majority of studies of surface contamination have been carried out in outbreak conditions or on high-dependency wards. Current surface cleaning guidance only requires surfaces to be visually clean. Microbiological standards for cleanliness have been proposed, however they are not widely adopted, and little implementation guidance is available. Evidence-based surface sampling protocols are required for the transmission risk surfaces pose to be adequately quantified and addressed.MethodsEnvironmental surface samples will be collected in a number of in- and outpatient settings, staff, and public areas, such as waiting rooms. This will be done before and after cleaning. Pathogens associated with nosocomial infection (e.g., ESKAPE pathogens, Clostridioides difficile and Candida auris) will be identified through culture methods and MALDI-ToF mass spectrometry. Antimicrobial susceptibility profiles of isolates will be determined following EUCAST protocols. Real-time PCR will be utilized to identify viral pathogens (including norovirus, adenovirus, influenza and SARS-CoV-2) present. Following this, samples will be collected for community composition sequencing, allowing for non-culturable microorganisms to be identified. Whole genome sequencing will be performed on any pathogens of interest isolated during this investigation.Results and ConclusionFewer microorganisms are expected to be isolated after cleaning than prior, and samples from in-patient environments will have higher proportions of pathogens. The hospital microbiome has rarely been investigated outside of outbreak conditions. This study presents a novel, systematic approach to assess the microorganisms present in the hospital environment, and how they are impacted by current cleaning measures. This will build a comprehensive picture of the hospital microflora and provide an evidence base for the development of surface sampling protocols, helping inform clinical risk assessments and subsequently improving patient outcomes.

Preface: Proceedings of the 4th International Conference on Bioscience and Biotechnology (4th ICBB 2021), 21st-23rd September 2021

Eka Sunarwidhi Prasedya, S.Si., M.Sc., Ph.D. Chairman of 4th ICBB 2021 This issue of IOP conference proceedings contains papers presented at the 4th International Conference on Bioscience and Biotechnology (ICBB) 2021. The ICBB is an annual international conference since 2018 that was initiated by Prof Ir H Sunarpi PhD. This year we are lucky to collaborate with Postgraduate-studies (Pascasarjana) University of Mataram thanks to the director Prof. Ir. H Muhamad Sarjan, M.Agr.,C.P. Ph.D and vice director Prof. Ir. Bambang Hari Kusumo, M.Agr.St., Ph.D. This meeting is hosted by Lab of Bioscience and Biotechnology Research, University of Mataram, Indonesia. It is held for three days, from 21 to 23 September 2021 by virtual conference with zoom platform due to COVID-19 pandemic. Interactive online presentations were arranged through Zoom Video Communications for the participants to present their ideas. The conference was divided into two main sessions: Main session for Keynote speakers and Panel Sessions for participants. A time of 30 minutes was given for Keynote speakers to present their fabulous work. For panel session, 10 minutes were given for participants to share their research and findings. A total of 204 participants (180 presenters and 24 non-presenters) from Universities, Research Institutes and also Government Departments joined the conference. All the selected papers were peer reviewed by expert reviewers in a double blind review system as per the review policy given by IOP Conference Series. On the first day of the conference (21st September) invited talks were presented by Prof. Julian Heyes, Ph.D. from Massey University New Zealand on “Deriving value from elite indigenous fruit and vegetable species”, Prof. Bambang Hari Kusumo, M.Agr.St., Ph.D. from University of Mataram on “Rapid measurement of soil carbon using near infrared technology”and Prof. Dr. Endang Semiarti, M.S., M.Sc. from Universitas Gadjah Mada Indonesia on “Biotechnology approach to improve the quality and quantity of orchids as potential agricultural commodities in Indonesia”. The second day of the conference presented talks by Prof. Lim Phaik Eem, Ph.D. from University of Malaya on “Importance of marine habitat conservation for utilization and discovery of new bioresources of seaweeds”, Prof. Mat Vanderklift, Ph.D. from Indian Ocean Marine Research Centre CSIRO Australia on “Opportunities for sustainable use of coastal ecosystems”, Assoc.Prof. Dr. Rapeeporn Ruangchuay from Prince of Songkla University Thailand on “ Seaweed resources in Thailand: cultivation and utilization” and Dr.rer.nat. Andri Frediansyah, M.Sc. from LIPI Indonesia on ”Microbial natural products: a discovery strategy”. The final day of the conference included talks by Prof. Akihiro Hazama, Ph.D. from Fukushima Medical University on “Investigation of cigarette smoke-induced cell hyperplasia mechanism using Induced Pluripotent Stem Cell (IPSCs)”, Prof. Kato Yasuhiro, Ph.D. from Keio University Japan on ”Water circulation of the earth and life” and Eka Sunarwidhi Prasedya, Ph.D. from University of Mataram Indonesia on “Microbiome implications for bioprospecting of seaweeds”. List of Conference Photograph, Conference Organizers are available in this pdf.

Coordinating and Assisting Research at the SARS-CoV-2/Microbiome Nexus.

Although the COVID-19 pandemic is caused by a single virus, the rest of the human microbiome appears to be involved in the disease and could influence vaccine responses while offering opportunities for microbiome-directed therapeutics. The newly formed Microbiome Centers Consortium (MCC) surveyed its membership and identified four ways to leverage the strengths and experience of microbiome centers in the response to the COVID-19 pandemic. To meet these needs, the MCC will provide a platform to coordinate clinical and environmental research, assist with practical obstacles, and help communicate the connections between the microbiome and COVID-19. We ask that microbiome researchers join us in these efforts to address the ongoing pandemic.