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Article ; Online: Research Note: Reticulocytes and related erythroid atypia of ducks-indicators of stress or pathology?

Cotter, Paul F

2023 Volume 103, Issue 2, Page(s) 103353

Abstract: ... TWBC) of the study set ranged from 5 K/μL (embryo E [d24]) to >100 K/μL (older ducks) with heterophil ...

Abstract	Two kinds of reticulocytes, and atypical erythroid cells, were found in the blood of apparently healthy ducks with Wright-Giemsa (W-G) stain. The reticulin of network-type examples (nRtc) is of a large complex (3-D) form. The punctate reticulocyte (pRtc) contains small pin-point cytoplasmic granulations; both cells are distinct from a polychromatic RBC (pRBC). Atypical erythroid cells with oval or irregular shapes reminiscent of primary or yolk-sac RBCs (ysRBC) accompanied the Rtc. Rare binuclear cells (bi) were either polychromatic (pRBC and pRtc) or full hemoglobin (Hb) types (RBC). Some bi with equal-sized daughter nuclei were presumed mitotic products. Conversely, unequal daughter nuclei were amitotic products, a nuclear division without chromosomes or a spindle. Erythrocytes formed tight aggregations with thrombocytes or other cells called "toroids"; further indicating a reactive hemogram. Erythroplastids (ep) anuclear erythroid cells, found along with other atypia, were either pRBC or full Hb types. The total white blood counts (TWBC) of the study set ranged from 5 K/μL (embryo E [d24]) to >100 K/μL (older ducks) with heterophil ratios (H/L) ranging from 0.5 to >4.0. Atypical erythroid cells, like atypical leukocytes, indicate a transition from homeostasis to a reactive state. Recognition of nRtc, pRtc, and toroids as reactive forms, expands the utility of hematologic data in assessing stress levels, indicating pathology, and exploring welfare questions. The present observations support earlier work showing some reticulocytes are detected by W-G alone and do not require vital dyes. Cells and behaviors described here demonstrate the benefit that a description of overall cytology adds to H/L ratios in evaluating a hemogram.
MeSH term(s)	Animals ; Reticulocytes ; Ducks ; Chickens ; Erythrocytes ; Leukocytes
Language	English
Publishing date	2023-12-05
Publishing country	England
Document type	Journal Article
ZDB-ID	242586-5
ISSN	1525-3171 ; 0032-5791
ISSN (online)	1525-3171
ISSN	0032-5791
DOI	10.1016/j.psj.2023.103353
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Article: Six areas of consideration when designing and conducting online surveys in microbiology for facilitating improved scientific communication.

Garcia-Gutierrez, Enriqueta / Walsh, Liam H / Cotter, Paul D

Frontiers in microbiology

2023 Volume 14, Page(s) 1288822

Language	English
Publishing date	2023-12-05
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2023.1288822
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Article ; Online: Fermented foods: Harnessing their potential to modulate the microbiota-gut-brain axis for mental health.

Balasubramanian, Ramya / Schneider, Elizabeth / Gunnigle, Eoin / Cotter, Paul D / Cryan, John F

Neuroscience and biobehavioral reviews

2024 Volume 158, Page(s) 105562

Abstract: Over the past two decades, whole food supplementation strategies have been leveraged to target mental health. In addition, there has been increasing attention on the ability of gut microbes, so called psychobiotics, to positively impact behaviour though ... ...

Abstract	Over the past two decades, whole food supplementation strategies have been leveraged to target mental health. In addition, there has been increasing attention on the ability of gut microbes, so called psychobiotics, to positively impact behaviour though the microbiota-gut-brain axis. Fermented foods offer themselves as a combined whole food microbiota modulating intervention. Indeed, they contain potentially beneficial microbes, microbial metabolites and other bioactives, which are being harnessed to target the microbiota-gut-brain axis for positive benefits. This review highlights the diverse nature of fermented foods in terms of the raw materials used and type of fermentation employed, and summarises their potential to shape composition of the gut microbiota, the gut to brain communication pathways including the immune system and, ultimately, modulate the microbiota-gut-brain axis. Throughout, we identify knowledge gaps and challenges faced in designing human studies for investigating the mental health-promoting potential of individual fermented foods or components thereof. Importantly, we also suggest solutions that can advance understanding of the therapeutic merit of fermented foods to modulate the microbiota-gut-brain axis.
MeSH term(s)	Humans ; Probiotics ; Brain-Gut Axis ; Mental Health ; Gastrointestinal Microbiome ; Fermented Foods
Language	English
Publishing date	2024-01-24
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	282464-4
ISSN	1873-7528 ; 0149-7634
ISSN (online)	1873-7528
ISSN	0149-7634
DOI	10.1016/j.neubiorev.2024.105562
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Article: Kefir4All, a citizen science initiative to raise awareness of the roles that microbes play in food fermentation.

Walsh, Liam H / Breselge, Samuel / Martin, José Guilherme Prado / Coakley, Mairéad / Ferguson, Eimear / Stapleton, Aimee / Crispie, Fiona / O'Toole, Paul W / Cotter, Paul D

Journal of microbiology & biology education

2024 Volume 25, Issue 1, Page(s) e0015523

Abstract: ... relating to microbiology, introduced through the medium of producing fermented food, i.e., milk kefir or ...

Abstract	Microorganisms are ubiquitous in nature and are central to human, animal, environmental, and planetary health. They play a particularly important role in the food chain and the production of high-quality, safe, and health-promoting foods, especially fermented foods. This important role is not always apparent to members of the public. Here, we describe Kefir4All, a citizen science project designed to provide the general public with an opportunity to expand their awareness, knowledge, and practical skills relating to microbiology, introduced through the medium of producing fermented food, i.e., milk kefir or water kefir. During the course of Kefir4All, 123 citizen scientists, from second-level school and non-school settings, participated in a study to track changes in the microbial composition of kefirs, by performing and recording details of milk kefir or water kefir fermentations they performed in their homes or schools over the 21-week project. At the start of the study, the citizen scientists were provided with milk or water kefir grains to initiate the fermentations. Both types of kefir grain are semi-solid, gelatinous-like substances, composed of exopolysaccharides and proteins, containing a symbiotic community of bacteria and yeast. The experimental component of the project was complemented by a number of education and outreach events, including career talks and a site visit to our research center (Kefir Day). At the end of the study, a report was provided to each citizen scientist, in which individualized results of their fermenting activities were detailed. A number of approaches were taken to obtain feedback and other insights from the citizen scientists. Evaluations took place before and after the Kefir4All project to gauge the citizen scientist's self-reported awareness, knowledge, and interest in microbiology and fermented foods. Further insights into the level of citizen science participation were gained through assessing the number of samples returned for analysis and the level of participation of the citizen scientists throughout the project. Notably, the survey results revealed a self-reported, increased interest in, and general knowledge of, science among the Kefir4All citizen scientists after undertaking the project and a willingness to take part in further citizen science projects. Ultimately, Kefir4All represents an example of the successful integration of citizen science into existing education and research systems.
Language	English
Publishing date	2024-01-03
Publishing country	United States
Document type	Journal Article
ISSN	1935-7877
ISSN	1935-7877
DOI	10.1128/jmbe.00155-23
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Article ; Online: Phlebotomy-free days in children hospitalized with common infections and their association with clinical outcomes.

Collins, Megan E / Hall, Matt / Shah, Samir S / Molloy, Matthew J / Aronson, Paul L / Cotter, Jillian M / Steiner, Michael J / McCoy, Elisha / Tchou, Michael J / Stephens, John R / Markham, Jessica L

Journal of hospital medicine

2024 Volume 19, Issue 4, Page(s) 251–258

Abstract: Background: Phlebotomy for hospitalized children has consequences (e.g., pain, iatrogenic anemia ...

Abstract	Background: Phlebotomy for hospitalized children has consequences (e.g., pain, iatrogenic anemia), and unnecessary testing is a modifiable source of waste in healthcare. Days without blood draws or phlebotomy-free days (PFDs) has the potential to serve as a hospital quality measure. Objective: To describe: (1) the frequency of PFDs in children hospitalized with common infections and (2) the association of PFDs with clinical outcomes. Design, settings and participants: We performed a cross-sectional study of children hospitalized 2018-2019 with common infections at 38 hospitals using the Pediatric Health Information System database. We included infectious All Patients Refined Diagnosis Related Groups with a median length of stay (LOS) >2 days. We excluded patients with medical complexity, interhospital transfers, those receiving intensive care, and in-hospital mortality. Main outcome and measures: We defined PFDs as hospital days (midnight to midnight) without laboratory blood testing and measured the proportion of PFDs divided by total hospital LOS (PFD ratio) for each condition and hospital. Higher PFD ratios signify more days without phlebotomy. Hospitals were grouped into low, moderate, and high average PFD ratios. Adjusted outcomes (LOS, costs, and readmissions) were compared across groups. Results: We identified 126,135 encounters. Bronchiolitis (0.78) and pneumonia (0.54) had the highest PFD ratios (most PFDs), while osteoarticular infections (0.28) and gastroenteritis (0.30) had the lowest PFD ratios. There were no differences in adjusted clinical outcomes across PFD ratio groups. Among children hospitalized with common infections, PFD ratios varied across conditions and hospitals, with no association with outcomes. Our data suggest overuse of phlebotomy and opportunities to improve the care of hospitalized children.
MeSH term(s)	Humans ; Child ; Phlebotomy/adverse effects ; Cross-Sectional Studies ; Length of Stay ; Pneumonia ; Hospitals
Language	English
Publishing date	2024-02-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	2233783-0
ISSN	1553-5606 ; 1553-5592
ISSN (online)	1553-5606
ISSN	1553-5592
DOI	10.1002/jhm.13282
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Article ; Online: Relevance of organ(s)-on-a-chip systems to the investigation of food-gut microbiota-host interactions.

Garcia-Gutierrez, Enriqueta / Cotter, Paul D

Critical reviews in microbiology

2021 Volume 48, Issue 4, Page(s) 463–488

Abstract: The ever greater understanding of the composition and function of the gut microbiome has provided new opportunities with respect to understanding and treating human disease. However, the models employed for in vitro and in vivo animal studies do not ... ...

Abstract	The ever greater understanding of the composition and function of the gut microbiome has provided new opportunities with respect to understanding and treating human disease. However, the models employed for in vitro and in vivo animal studies do not always provide the required insights. As a result, one such alternative in vitro cell culture based system, organ-on-a-chip technology, has recently attracted attention as a means of obtaining data that is representative of responses in humans. Organ-on-a-chip systems are designed to mimic the interactions of different tissue elements that were missing from traditional two-dimensional tissue culture. While they do not traditionally include a microbiota component, organ-on-a-chip systems provide a potentially valuable means of characterising the interactions between the microbiome and human tissues with a view to providing even greater accuracy. From a dietary perspective, these microbiota-organ-on-a-chip combinations can help researchers to predict how the consumption of specific foods and ingredients can impact on human health and disease. We provide an overview of the relevance and interactions of the gut microbiota and the diet in human health, we summarise the components involved in the organ-on-a-chip systems, how these systems have been employed for microbiota based studies and their potential relevance to study the interplay between food-gut microbiota-host interactions.
MeSH term(s)	Animals ; Diet ; Gastrointestinal Microbiome ; Host Microbial Interactions ; Humans ; Lab-On-A-Chip Devices ; Microbiota
Language	English
Publishing date	2021-09-30
Publishing country	England
Document type	Journal Article
ZDB-ID	1053620-6
ISSN	1549-7828 ; 1040-841X
ISSN (online)	1549-7828
ISSN	1040-841X
DOI	10.1080/1040841X.2021.1979933
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Article ; Online: Fermented foods and gastrointestinal health: underlying mechanisms.

Mukherjee, Arghya / Breselge, Samuel / Dimidi, Eirini / Marco, Maria L / Cotter, Paul D

Nature reviews. Gastroenterology & hepatology

2023 Volume 21, Issue 4, Page(s) 248–266

Abstract: Although fermentation probably originally developed as a means of preserving food substrates, many fermented foods (FFs), and components therein, are thought to have a beneficial effect on various aspects of human health, and gastrointestinal health in ... ...

Abstract	Although fermentation probably originally developed as a means of preserving food substrates, many fermented foods (FFs), and components therein, are thought to have a beneficial effect on various aspects of human health, and gastrointestinal health in particular. It is important that any such perceived benefits are underpinned by rigorous scientific research to understand the associated mechanisms of action. Here, we review in vitro, ex vivo and in vivo studies that have provided insights into the ways in which the specific food components, including FF microorganisms and a variety of bioactives, can contribute to health-promoting activities. More specifically, we draw on representative examples of FFs to discuss the mechanisms through which functional components are produced or enriched during fermentation (such as bioactive peptides and exopolysaccharides), potentially toxic or harmful compounds (such as phytic acid, mycotoxins and lactose) are removed from the food substrate, and how the introduction of fermentation-associated live or dead microorganisms, or components thereof, to the gut can convey health benefits. These studies, combined with a deeper understanding of the microbial composition of a wider variety of modern and traditional FFs, can facilitate the future optimization of FFs, and associated microorganisms, to retain and maximize beneficial effects in the gut.
MeSH term(s)	Humans ; Fermented Foods ; Gastrointestinal Tract ; Fermentation
Language	English
Publishing date	2023-12-11
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2493722-8
ISSN	1759-5053 ; 1759-5045
ISSN (online)	1759-5053
ISSN	1759-5045
DOI	10.1038/s41575-023-00869-x
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Article ; Online: A reduced potential for lameness bacterial transmission by Lucilia sericata larvae and flies through metamorphosis.

Curwen, Alice E / Still, Rebecca L / Angell, Joseph W / Eady, Paul E / Millson, Stefan H / Staton, Gareth J / Evans, Nicholas J / Duncan, Jennifer S / Cotter, Sheena C / Clegg, Simon R

Research in veterinary science

2023 Volume 163, Page(s) 104967

Abstract: Lameness in sheep is one of the most serious issues on farms in the UK and worldwide, affecting over 90% of all UK sheep flocks. Despite its severity and prevalence, there are knowledge gaps regarding transmission routes of bacterial pathogens associated ...

Abstract	Lameness in sheep is one of the most serious issues on farms in the UK and worldwide, affecting over 90% of all UK sheep flocks. Despite its severity and prevalence, there are knowledge gaps regarding transmission routes of bacterial pathogens associated with infectious lameness in sheep. As larvae of Lucilia sericata are commonly found on foot lesions on lame sheep, it was hypothesised that the flies or their larvae could harbour lameness associated bacteria. This study examined the gut contents of larvae obtained from the foot lesions of lame sheep and compared them to control larvae collected from infested cat food on the same farm. Of particular interest, were the presence of three different bacterial genera associated with lameness; Fusobacterium necrophorum, Dichelobacter nodosus and Treponema spp., for which viability was also investigated. Larvae were cultured In vitro and some allowed to metamorphose into flies before specific PCR assays were carried out on the gut contents. Results showed a significant association between the bacteria on the feet of the sheep and those within the larvae. Although the gut contents of all larvae found on sheep feet contained one or more of the lameness bacteria, none of the bacteria were recovered from the adult flies, suggesting a level of gut remodelling during metamorphosis. Interestingly, Treponema spp. and Fusobacterium spp. were viable when isolated from gut contents of larvae. Maintenance of infection from larvae to fly did not occur. However, it still remains important to control both disease and insect populations of farms to maintain animal welfare.
MeSH term(s)	Sheep ; Animals ; Cats ; Foot Rot ; Diptera ; Larva ; Lameness, Animal ; Sheep Diseases/epidemiology ; Bacteria ; Cat Diseases
Language	English
Publishing date	2023-08-02
Publishing country	England
Document type	Journal Article
ZDB-ID	840961-4
ISSN	1532-2661 ; 0034-5288
ISSN (online)	1532-2661
ISSN	0034-5288
DOI	10.1016/j.rvsc.2023.104967
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Article: Seasonal variation in the Canastra cheese mycobiota.

Martin, José Guilherme Prado / Silva, João Marcos Maia / César, Isabel Cristina da Rocha / da Silva, Meiriele / Santana, Samara Aparecida / Veloso, Tomás Gomes Reis / Silva, Jonas Guimarães E / Ferreira, Celia Lucia de Luces Fortes / Leech, John / Cotter, Paul D

Frontiers in microbiology

2023 Volume 13, Page(s) 1076672

Abstract: Canastra cheese is the most well-known artisanal cheese produced in Brazil. Although its production includes a step to remove fungi from the cheese surface, in recent years some cheesemakers have preserved the autochthonous fungi grown during ripening ... ...

Abstract	Canastra cheese is the most well-known artisanal cheese produced in Brazil. Although its production includes a step to remove fungi from the cheese surface, in recent years some cheesemakers have preserved the autochthonous fungi grown during ripening due to an interest in the sensory characteristics attributed to these microorganisms. In this work, the mycobiota of artisanal cheeses produced in the Canastra region was characterized based on ITS marker gene analysis. A total of 96 artisanal cheeses from 16 different farms across 9 cities were collected during two different periods (dry and wet seasons). The Canastra cheese mycobiota was significantly impacted by the season, the city of production and the farm but altitude did not affect the fungal community of the cheeses analyzed.
Language	English
Publishing date	2023-02-03
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2022.1076672
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Article ; Online: Variation in stool testing for children with acute gastrointestinal infections.

Markham, Jessica L / Hall, Matt / Collins, Megan E / Shah, Samir S / Molloy, Matthew J / Aronson, Paul L / Cotter, Jillian M / Steiner, Michael J / McCoy, Elisha / Tchou, Michael J / Stephens, John R

Journal of hospital medicine

2023 Volume 18, Issue 6, Page(s) 473–482

Abstract: ... in stool testing rates across hospitals, particularly during encounters for hospitalized children (e.g ...

Abstract	Background and objective: Children with gastrointestinal infections often require acute care.The objectives of this study were to describe variations in patterns of stool testing across children's hospitals and determine whether such variation was associated with utilization outcomes. Design, settings and participants: We performed a multicenter, cross-sectional study using the Pediatric Health Information System (PHIS) database. We identified stool testing (multiplex polymerase chain reaction [PCR], stool culture, ova and parasite, Clostridioides difficile, and other individual stool bacterial or viral tests) in children diagnosed with acute gastrointestinal infections. Main outcome and measures: We calculated the overall testing rates and hospital-level stool testing rates, stratified by setting (emergency department [ED]-only vs. hospitalized). We stratified individual hospitals into low, moderate, or high testing institutions. Generalized estimating equations were then used to examine the association of hospital testing groups and outcomes, specifically, length of stay (LOS), costs, and revisit rates. Results: We identified 498,751 ED-only and 40,003 encounters for hospitalized children from 2016 to 2020. Compared to ED-only encounters, stool studies were obtained with increased frequency among encounters for hospitalized children (ED-only: 0.1%-2.3%; Hospitalized: 1.5%-13.8%, all p < 0.001). We observed substantial variation in stool testing rates across hospitals, particularly during encounters for hospitalized children (e.g., rates of multiplex PCRs ranged from 0% to 16.8% for ED-only and 0% to 65.0% for hospitalized). There were no statistically significant differences in outcomes among low, moderate, or high testing institutions in adjusted models. Conclusions: Children with acute gastrointestinal infections experience substantial variation in stool testing within and across hospitals, with no difference in utilization outcomes. These findings highlight the need for guidelines to address diagnostic stewardship.
MeSH term(s)	Child ; Humans ; Retrospective Studies ; Cross-Sectional Studies ; Length of Stay ; Communicable Diseases
Language	English
Publishing date	2023-03-29
Publishing country	United States
Document type	Multicenter Study ; Journal Article
ZDB-ID	2233783-0
ISSN	1553-5606 ; 1553-5592
ISSN (online)	1553-5606
ISSN	1553-5592
DOI	10.1002/jhm.13087
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