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15 pages, 1942 KiB

Open AccessArticle

A Bioinformatics Approach to Mine the Microbial Proteomic Profile of COVID-19 Mass Spectrometry Data

by Aziz Abdullah A. Alnakli, Amara Jabeen, Rajdeep Chakraborty, Abidali Mohamedali and Shoba Ranganathan

Appl. Microbiol. 2022, 2(1), 150-164; https://doi.org/10.3390/applmicrobiol2010010 - 03 Feb 2022

Cited by 2 | Viewed by 2837

Abstract

Mass spectrometry (MS) is one of the key technologies used in proteomics. The majority of studies carried out using proteomics have focused on identifying proteins in biological samples such as human plasma to pin down prognostic or diagnostic biomarkers associated with particular conditions [...] Read more.

Mass spectrometry (MS) is one of the key technologies used in proteomics. The majority of studies carried out using proteomics have focused on identifying proteins in biological samples such as human plasma to pin down prognostic or diagnostic biomarkers associated with particular conditions or diseases. This study aims to quantify microbial (viral and bacterial) proteins in healthy human plasma. MS data of healthy human plasma were searched against the complete proteomes of all available viruses and bacteria. With this baseline established, the same strategy was applied to characterize the metaproteomic profile of different SARS-CoV-2 disease stages in the plasma of patients. Two SARS-CoV-2 proteins were detected with a high confidence and could serve as the early markers of SARS-CoV-2 infection. The complete bacterial and viral protein content in SARS-CoV-2 samples was compared for the different disease stages. The number of viral proteins was found to increase significantly with the progression of the infection, at the expense of bacterial proteins. This strategy can be extended to aid in the development of early diagnostic tests for other infectious diseases based on the presence of microbial biomarkers in human plasma samples. Full article

(This article belongs to the Special Issue Human Microbiota Influence on Human Health Status)

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28 pages, 970 KiB

Open AccessArticle

Nourishing the Human Holobiont to Reduce the Risk of Non-Communicable Diseases: A Cow’s Milk Evidence Map Example

by Rodney R. Dietert, Margaret E. Coleman, D. Warner North and Michele M. Stephenson

Appl. Microbiol. 2022, 2(1), 25-52; https://doi.org/10.3390/applmicrobiol2010003 - 30 Dec 2021

Cited by 4 | Viewed by 4251

Abstract

The microbiome revolution brought the realization that diet, health, and safety for humans in reality means diet, health, and safety for the human holobiont/superorganism. Eating healthier means much more than just feeding human cells. Our diet must also nourish the combination of our [...] Read more.

The microbiome revolution brought the realization that diet, health, and safety for humans in reality means diet, health, and safety for the human holobiont/superorganism. Eating healthier means much more than just feeding human cells. Our diet must also nourish the combination of our microbiome and our connected physiological systems (e.g., the microimmunosome). For this reason, there has been an interest in returning to ancestral “complete” unprocessed foods enriched in microbes, including raw milks. To contribute to this inevitable “nourishing the holobiont” trend, we introduce a systematic risk–benefit analysis tool (evidence mapping), which facilitates transdisciplinary state-of-the-science decisions that transcend single scientific disciplines. Our prior paper developed an evidence map (a type of risk–benefit mind map) for raw vs. processed/pasteurized human breast milk. In the present paper, we follow with a comprehensive evidence map and narrative for raw/natural vs. processed/pasteurized cow’s milk. Importantly, the evidence maps incorporate clinical data for both infectious and non-communicable diseases and allow the impact of modern agricultural, food management, and medical and veterinary monitoring outcomes to be captured. Additionally, we focus on the impact of raw milks (as “complete” foods) on the microimmunosome, the microbiome-systems biology unit that significantly determines risk of the world’s number one cause of human death, non-communicable diseases. Full article

(This article belongs to the Special Issue Human Microbiota Influence on Human Health Status)

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27 pages, 1754 KiB

Open AccessArticle

Enhancing Human Superorganism Ecosystem Resilience by Holistically ‘Managing Our Microbes’

by Margaret E. Coleman, Rodney R. Dietert, D. Warner North and Michele M. Stephenson

Appl. Microbiol. 2021, 1(3), 471-497; https://doi.org/10.3390/applmicrobiol1030031 - 18 Oct 2021

Cited by 4 | Viewed by 4406

Abstract

Microbes in the 21st century are understood as symbionts ‘completing’ the human ‘superorganism’ (Homo sapiens plus microbial partners-in-health). This paper addresses a significant paradox: despite the vast majority of our genes being microbial, the lack of routine safety testing for the microbiome [...] Read more.

Microbes in the 21st century are understood as symbionts ‘completing’ the human ‘superorganism’ (Homo sapiens plus microbial partners-in-health). This paper addresses a significant paradox: despite the vast majority of our genes being microbial, the lack of routine safety testing for the microbiome has led to unintended collateral side effects from pharmaceuticals that can damage the microbiome and inhibit innate ‘colonization resistance’ against pathobionts. Examples are discussed in which a Microbiome First Medicine approach provides opportunities to ‘manage our microbes’ holistically, repair dysbiotic superorganisms, and restore health and resilience in the gut and throughout the body: namely, managing nosocomial infections for Clostridioides difficile and Staphylococcus aureus and managing the gut and neural systems (gut–brain axis) in autism spectrum disorder. We then introduce a risk analysis tool: the evidence map. This ‘mapping’ tool was recently applied by us to evaluate evidence for benefits, risks, and uncertainties pertaining to the breastmilk ecosystem. Here, we discuss the potential role of the evidence map as a risk analysis methodology to guide scientific and societal efforts to: (1) enhance ecosystem resilience, (2) ‘manage our microbes’, and (3) minimize the adverse effects of both acute and chronic diseases. Full article

(This article belongs to the Special Issue Human Microbiota Influence on Human Health Status)

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18 pages, 1435 KiB

Open AccessArticle

Examining Evidence of Benefits and Risks for Pasteurizing Donor Breastmilk

by Margaret E. Coleman, D. Warner North, Rodney R. Dietert and Michele M. Stephenson

Appl. Microbiol. 2021, 1(3), 408-425; https://doi.org/10.3390/applmicrobiol1030027 - 23 Sep 2021

Cited by 4 | Viewed by 4552

Abstract

An evidence map is visualized as a starting point for deliberations by trans-disciplinary stakeholders, including microbiologists with interests in the evidence and its influence on health and safety. Available evidence for microbial benefits and risks of the breastmilk ecosystem was structured as an [...] Read more.

An evidence map is visualized as a starting point for deliberations by trans-disciplinary stakeholders, including microbiologists with interests in the evidence and its influence on health and safety. Available evidence for microbial benefits and risks of the breastmilk ecosystem was structured as an evidence map using established risk analysis methodology. The evidence map based on the published literature and reports included the evidence basis, pro- and contra-arguments with supporting and attenuating evidence, supplemental studies on mechanisms, overall conclusions, and remaining uncertainties. The evidence basis for raw breastmilk included one benefit–risk assessment, systematic review, and systematic review/meta-analysis, and two cohort studies. The evidence basis for benefits was clear, convincing, and conclusive, with supplemental studies on plausible mechanisms attributable to biologically active raw breastmilk. Limited evidence was available to assess microbial risks associated with raw breastmilk and pasteurized donor milk. The evidence map provides transparent communication of the ‘state-of-the-science’ and uncertainties for microbial benefits and risks associated with the breastmilk microbiota to assist in deeper deliberations of the evidence with decision makers and stakeholders. The long-term aims of the evidence map are to foster deliberation, motivate additional research and analysis, and inform future evidence-based policies about pasteurizing donor breastmilk. Full article

(This article belongs to the Special Issue Human Microbiota Influence on Human Health Status)

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31 pages, 3050 KiB

Open AccessArticle

Kefir Culture-Mediated Fermentation to Improve Phenolic-Linked Antioxidant, Anti-Hyperglycemic and Human Gut Health Benefits in Sprouted Food Barley

by Ramnarain Ramakrishna, Dipayan Sarkar, Munevver Dogramaci and Kalidas Shetty

Appl. Microbiol. 2021, 1(2), 377-407; https://doi.org/10.3390/applmicrobiol1020026 - 17 Sep 2021

Cited by 3 | Viewed by 3779

Abstract

The bioprocessing strategy is an effective approach to improve bioavailability and stability of bioactive compounds for designing functional foods and ingredients. In this study, food barley was bio-transformed to improve functional bioactives by sprouting, coupled with beneficial lactic acid bacteria (LAB)-based fermentation. Dairy [...] Read more.

The bioprocessing strategy is an effective approach to improve bioavailability and stability of bioactive compounds for designing functional foods and ingredients. In this study, food barley was bio-transformed to improve functional bioactives by sprouting, coupled with beneficial lactic acid bacteria (LAB)-based fermentation. Dairy Kefir culture with mixed beneficial LAB strains was targeted to ferment aqueous slurries of sprouted hulless food barley flour (unpigmented, purple, and black barley) for 72 h, and modulation of phenolic-linked antioxidant and anti-hyperglycemic functionalities were evaluated using in vitro assay models. The biochemical parameters analyzed were total soluble phenolic (TSP) content, profile of phenolic compounds, total antioxidant activity, and anti-hyperglycemic property-relevant α-amylase and α-glucosidase enzyme inhibitory activities. Furthermore, human gut health benefits of relevant properties of fermented slurries of barley flour were also evaluated based on growth of Kefir culture and subsequent determination of anti-bacterial potential against pathogenic human ulcer causing bacteria Helicobacter pylori. Kefir culture-mediated fermentation of 48-h sprouted barley flours improved the TSP content and associated antioxidant and anti-hyperglycemic functionalities. Additionally, anti-bacterial potential against H. pylori and sustaining active growth of viable LAB cells above the minimum level required for probiotic activity were also observed in fermented food barley flour slurries. Full article

(This article belongs to the Special Issue Human Microbiota Influence on Human Health Status)

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19 pages, 2798 KiB

Open AccessArticle

Improving Phenolic-Linked Antioxidant, Antihyperglycemic and Antibacterial Properties of Emmer and Conventional Wheat Using Beneficial Lactic Acid Bacteria

by Ashish Christopher, Dipayan Sarkar and Kalidas Shetty

Appl. Microbiol. 2021, 1(2), 270-288; https://doi.org/10.3390/applmicrobiol1020020 - 21 Jul 2021

Cited by 3 | Viewed by 3023

Abstract

Beneficial lactic acid bacteria (LAB)-based fermentation is an effective bioprocessing approach to improve human-health-targeted functional benefits of plant-based food substrates, such as cereal grains. Previously, we observed high phenolic bioactive-linked antioxidant and anti-hyperglycemic properties in whole grain Emmer (hulled). In this study, beneficial [...] Read more.

Beneficial lactic acid bacteria (LAB)-based fermentation is an effective bioprocessing approach to improve human-health-targeted functional benefits of plant-based food substrates, such as cereal grains. Previously, we observed high phenolic bioactive-linked antioxidant and anti-hyperglycemic properties in whole grain Emmer (hulled). In this study, beneficial LAB (Lactiplantibacillus plantarum) was recruited to ferment (0–72 h) aqueous extracts (0.4 g/mL concentration) of previously optimized hulled Emmer wheat and conventional red spring wheat cv. Barlow. The fermented and unfermented (control) wheat extracts were analyzed for phenolic content, phenolic profile, antioxidant activity, and antihyperglycemic properties (α-amylase and α-glucosidase enzyme inhibitory activity) using in vitro assay models. Additionally, antimicrobial activity against pathogenic bacteria Helicobacter pylori, and potential prebiotic activity supporting the growth of beneficial Bifidobacterium longum were also investigated. Improvement in antioxidant activity and antihyperglycemic functional benefits were observed, while soluble phenolic content remained high after 72 h fermentation. Antimicrobial activity against H. pylori was also observed in 48 and 72 h fermented wheat extracts. This study provides an insight into the efficacy of LAB-based fermentation as a safe bioprocessing tool to design health-targeted functional foods and ingredients from underutilized whole grains like Emmer for targeting type 2 diabetes dietary benefits. Full article

(This article belongs to the Special Issue Human Microbiota Influence on Human Health Status)

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12 pages, 1259 KiB

Open AccessArticle

Nasopharyngeal Microbiome Community Composition and Structure Is Associated with Severity of COVID-19 Disease and Breathing Treatment

by Amy K. Feehan, Rebecca Rose, David J. Nolan, Austin M. Spitz, Karlis Graubics, Rita R. Colwell, Julia Garcia-Diaz and Susanna L. Lamers

Appl. Microbiol. 2021, 1(2), 177-188; https://doi.org/10.3390/applmicrobiol1020014 - 05 Jul 2021

Cited by 9 | Viewed by 6561

Abstract

Viral infections are known to modulate the upper respiratory tract microbiome, but few studies have addressed differences in the nasopharyngeal microbiome following SARS-CoV-2 infection. Using nasopharyngeal swab medical waste samples from 79 confirmed SARS-CoV-2 positive and 20 SARS-CoV-2 negative patients, we assessed microbiome [...] Read more.

Viral infections are known to modulate the upper respiratory tract microbiome, but few studies have addressed differences in the nasopharyngeal microbiome following SARS-CoV-2 infection. Using nasopharyngeal swab medical waste samples from 79 confirmed SARS-CoV-2 positive and 20 SARS-CoV-2 negative patients, we assessed microbiome composition with metagenomic sequencing. COVID-19 status and breathing assistive device use was associated with differences in beta diversity, principal component analyses, community composition and abundance of several species. Serratia more frequently appeared in COVID-19 patient samples compared to negative patient samples, and Serratia, Streptococcus, Enterobacter, Veillonella, Prevotella, and Rothia appeared more frequently in samples of those who used breathing assistive devices. Smoking and age were associated with differences in alpha diversity. Cross-sectional differences in the microbiome were apparent with SARS-CoV-2 infection, but longitudinal studies are needed to understand the dynamics of viral and breathing treatment modulation of microbes. Full article

(This article belongs to the Special Issue Human Microbiota Influence on Human Health Status)

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7 pages, 387 KiB

Open AccessCase Report

Lincomycin Administration against Persistent Multi-Drug Resistant Chronic Endometritis in Infertile Women with a History of Repeated Implantation Failure

by Kotaro Kitaya and Tomomoto Ishikawa

Appl. Microbiol. 2022, 2(3), 554-560; https://doi.org/10.3390/applmicrobiol2030043 - 06 Aug 2022

Cited by 3 | Viewed by 1814

Abstract

Chronic endometritis (CE) is an infectious disease of the uterine lining, which is characterized by endometrial stromal plasmacyte (ESPC) infiltration. CE is often seen in infertile women with a history of repeated implantation failure (RIF) following an in vitro fertilization-embryo transfer program, recurrent [...] Read more.

Chronic endometritis (CE) is an infectious disease of the uterine lining, which is characterized by endometrial stromal plasmacyte (ESPC) infiltration. CE is often seen in infertile women with a history of repeated implantation failure (RIF) following an in vitro fertilization-embryo transfer program, recurrent pregnancy loss, and unknown etiology. Oral antibiotic agents, such as doxycycline, metronidazole, ciprofloxacin, azithromycin, and moxifloxacin, have been prescribed and are effective in the treatment of CE. Multi-drug resistance (MDR), however, is an emerging issue, as in other medical fields. We report six cases of persistent MDR-CE in infertile women who were resistant to all the aforementioned antibiotic agents. The bacterial genera and microbial communities unique to persistent MDR-CE were not identified in their vaginal secretions and/or endometrial fluid. Oral lincomycin administration (14 days, 1500 mg/day) was effective in the eradication of ESPCs in these women. In the embryo transfer cycles following histopathologic confirmation of cure (elimination of ESPCs) of persistent MDR-CE, three out of them had a successful live birth. Full article

(This article belongs to the Special Issue Human Microbiota Influence on Human Health Status)

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