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Article ; Online: Changes in gut bacterial communities and the incidence of antibiotic resistance genes during degradation of antibiotics by black soldier fly larvae

Cuncheng Liu / Huaiying Yao / Stephen J. Chapman / Jianqiang Su / Cunwen Wang

Environment International, Vol 142, Iss , Pp 105834- (2020)

2020

Abstract: As a saprophytic insect, the black soldier fly can digest organic waste efficiently in an environmentally friendly way. However, the ability and efficiency of this insect, and the microbial mechanisms involved, in the degradation of antibiotics are ... ...

Abstract	As a saprophytic insect, the black soldier fly can digest organic waste efficiently in an environmentally friendly way. However, the ability and efficiency of this insect, and the microbial mechanisms involved, in the degradation of antibiotics are largely uncharacterized. To obtain further details during the degradation of OTC (oxytetracycline) by black soldier fly larvae (larvae), the changes in intestinal bacterial communities were examined. Both ARGs (antibiotic resistance genes) and MGEs (mobile genetic elements) were found within the larval guts. At the end of the degradation period, 82.7%, 77.6% and 69.3% of OTC was degraded by larvae when the initial concentrations were 100, 1000 and 2000 mg kg−1 (dry weight), respectively, which was much higher than the degradation efficiencies (19.3–22.2%) without larvae. There was no obvious effect of OTC on the development of the larvae. Although the larval gut microorganisms were affected by OTC, they adapted to the altered environment. Enterococcus, Ignatzschineria, Providencia, Morganella, Paenalcaligenes and Actinomyces in the gut responded strongly to antibiotic exposure. Interestingly, numerous ARGs (specifically, 180 ARGs and 10 MGEs) were discovered, and significantly correlated with those of both integron-integrase gene and transposases in the larval gut. Of all the detected ARGs, tetracycline resistance genes expressed at relatively high levels and accounted for up to 67% of the total ARGs. In particular, Enterococcus, Ignatzschineria, Bordetella, Providencia and Proteus were all hosts of enzymatic modification genes of tetracycline in the guts that enabled effective degradation of OTC. These findings demonstrate that OTC can be degraded effectively and prove that the bioremediation of antibiotic contamination is enhanced by larvae. In addition, the abundance of ARGs and MGEs formed should receive attention and be considered in environmental health risk assessment systems.
Keywords	Black soldier fly larvae ; Antibiotic ; Antibiotic resistance genes (ARGs) ; Gut microorganisms ; Degradation ; Environmental sciences ; GE1-350
Subject code	610
Language	English
Publishing date	2020-09-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Non-invasive, vagus nerve stimulation to reduce ileus after colorectal surgery

Deborah D Stocken / Stephen J Chapman / Carolyn J Czoski Murray / Damian Tolan / Maureen Naylor / David G Jayne

BMJ Open, Vol 11, Iss

protocol for a feasibility trial with nested mechanistic studies

2021 Volume 7

Abstract: Introduction Ileus is a common and distressing condition characterised by gut dysfunction after surgery. While a number of interventions have aimed to curtail its impact on patients and healthcare systems, ileus is still an unmet challenge. Electrical ... ...

Abstract	Introduction Ileus is a common and distressing condition characterised by gut dysfunction after surgery. While a number of interventions have aimed to curtail its impact on patients and healthcare systems, ileus is still an unmet challenge. Electrical stimulation of the vagus nerve is a promising new treatment due to its role in modulating the neuro-immune axis through a novel anti-inflammatory reflex. The protocol for a feasibility study of non-invasive vagus nerve stimulation (nVNS), and a programme of mechanistic and qualitative studies, is described.Methods and analysis This is a participant-blinded, parallel-group, randomised, sham-controlled feasibility trial (IDEAL Stage 2b) of self-administered nVNS. One hundred forty patients planned for elective, minimally invasive, colorectal surgery will be randomised to four schedules of nVNS before and after surgery. Feasibility outcomes include assessments of recruitment and attrition, adequacy of blinding and compliance to the intervention. Clinical outcomes include bowel function and length of hospital stay. A series of mechanistic substudies exploring the impact of nVNS on inflammation and bowel motility will inform the design of the final stimulation schedule. Semistructured interviews with participants will explore experiences and perceptions of the intervention, while interviews with patients who decline participation will explore barriers to recruitment.Ethics and dissemination The protocol has been approved by the Tyne and Wear South National Health Service (NHS) Research Ethics Committee (19/NE/0217) on 2 July 2019. Feasibility, mechanistic and qualitative findings will be disseminated to national and international partners through peer-reviewed publications, academic conferences, social media channels and stakeholder engagement activities. The findings will build a case for or against progression to a definitive randomised assessment as well as informing key elements of study design.Trial registration number ISRCTN62033341.
Keywords	Medicine ; R
Subject code	420
Language	English
Publishing date	2021-07-01T00:00:00Z
Publisher	BMJ Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Incorporation of 13C-labelled rice rhizodeposition into soil microbial communities under different fertilizer applications

Wang, Juan / Huaiying Yao / Stephen J. Chapman

Applied soil ecology. 2016 May, v. 101

2016

Abstract: The application of nitrogen fertilizer is an important agronomic practice for stimulating plant production but is also reported to affect soil microorganisms, either directly or indirectly, via increased plant root exudation. In order to investigate the ... ...

Abstract	The application of nitrogen fertilizer is an important agronomic practice for stimulating plant production but is also reported to affect soil microorganisms, either directly or indirectly, via increased plant root exudation. In order to investigate the effect of nitrogen fertilizer on microorganisms utilizing root exudates, we chose three nitrogen application levels (0, 100, 200mgkg−1N) in a rice planted system and labelled the rice plants with continuous 13CO2. Phospholipid fatty acids (PLFA) were then extracted and determined by gas chromatography–combustion–isotope ratio mass spectrometry (GC–C–IRMS). Results showed that nitrogen application increased rice biomass and enhanced the δ13C value of the rice plant stem, root and soil. PLFA results suggested that nitrogen alone did not alter the microbial biomass and community structure directly, but that rice plant growth enhanced the microbial biomass and altered the microbial community structure greatly. The difference in microbial community structure between planted and unplanted treatments was mainly due to a higher percentage of the PLFAs 18:2ω6,9 and 16:0 and a lower percentage of i16:0 and a15:0 in the planted treatment. For planted treatments, nitrogen application significantly enhanced the total amount of 13C label and altered the microbial community which utilized the root exudates. Our results suggest that the nitrogen effect on the microbial community utilization of labelled materials was mediated by increased root rhizodeposition and provided evidence that fungi and Gram-negative bacteria were the main consumers of rice root exudates. We conclude that the impact of rice rhizodeposition on the soil microbial community utilization of root exudates is modified by nitrogen fertilizer application based on the 13C-PLFA results.
Keywords	community structure ; exudation ; fertilizer rates ; fungi ; Gram-negative bacteria ; mass spectrometry ; microbial biomass ; microbial communities ; nitrogen ; nitrogen fertilizers ; phospholipid fatty acids ; plant growth ; planting ; rhizodeposition ; rice ; root exudates ; soil ; soil microorganisms
Language	English
Dates of publication	2016-05
Size	p. 11-19.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	1196758-4
ISSN	0929-1393
ISSN	0929-1393
DOI	10.1016/j.apsoil.2016.01.010
Database	NAL-Catalogue (AGRICOLA)

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Article: Nitrification and nitrifiers in acidic soils

Li, Yaying / Graeme W. Nicol / Huaiying Yao / Stephen J. Chapman

Elsevier Ltd Soil biology & biochemistry. 2018 Jan., v. 116

2018

Abstract: Nitrification, as a crucial step in nitrogen cycling and plant nutrition, is a biologically mediated process responsible for enormous losses of nitrogen fertilizer and a contributor to environmental pollution. The recent progress in our understanding of ... ...

Abstract	Nitrification, as a crucial step in nitrogen cycling and plant nutrition, is a biologically mediated process responsible for enormous losses of nitrogen fertilizer and a contributor to environmental pollution. The recent progress in our understanding of nitrification and nitrifiers, specifically in acidic soils, is discussed and reviewed. At one time it was assumed that rates of nitrification are relatively low in acidic soils. However, more recent studies have demonstrated nitrification down to pH 3.0 and that the rate of nitrification can equal, or even exceed, that found in neutral soils. Studies on acidic forest soils in Europe noted that they have a high potential for nitrate production. Furthermore, using the 15N isotope-dilution technique it was shown that net nitrification measurements can markedly underestimate gross nitrification in these natural and highly organic systems. Using selective inhibitors it has been demonstrated that heterotrophic nitrifiers can contribute to nitrification. While heterotrophic nitrification can be performed by a wide range of bacteria and fungi, inhibitor studies point to fungi to be mainly responsible. Autotrophic ammonia-oxidizing bacteria (AOB), such as Nitrosomonas and Nitrosospira, have been known for some considerable time but have generally found to be inactive in acidic conditions. The discovery of ammonia monooxygenase in uncultured archaea that were functionally active at low pH pointed to an autotrophic microbial group (ammonia oxidizing archaea, AOA) that might be adapted to low substrate (ammonia) concentrations and responsible for nitrification in the wider range of acidic grassland and cultivated soils. Obligately acidophilic AOA have more recently been cultivated while stable isotope probing has been used to confirm the dominance of AOA over AOB in acidic soils. Detailed molecular studies using both 16S rRNA and amoA (ammonia monooxygenase sub-unit A) gene sequencing are continuing to expand our appreciation of the diversity of both AOB and AOA and how this varies over different pH ranges and in different ecosystems. Similar work is being directed towards nitrite oxidizing bacteria (NOB) but to date we do not fully know the role of pH in controlling NOB activity. Such understanding of nitrification and nitrifiers will help develop new effective nitrification inhibitors and aid the management of nitrogen cycling in acidic soils.
Keywords	acid soils ; ammonia ; ammonia monooxygenase ; Archaea ; ecosystems ; fungi ; grasslands ; heterotrophs ; isotope labeling ; nitrates ; nitrification ; nitrification inhibitors ; nitrifying bacteria ; nitrites ; nitrogen cycle ; nitrogen fertilizers ; Nitrosomonas ; Nitrosospira ; pH ; plant nutrition ; pollution ; ribosomal RNA ; sequence analysis ; stable isotopes ; Europe
Language	English
Dates of publication	2018-01
Size	p. 290-301.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	280810-9
ISSN	0038-0717
ISSN	0038-0717
DOI	10.1016/j.soilbio.2017.10.023
Database	NAL-Catalogue (AGRICOLA)

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Article: Soil and tree biomass carbon sequestration potential of silvopastoral and woodland-pasture systems in North East Scotland

Beckert, Marvin R / Pete Smith / Allan Lilly / Stephen J. Chapman

Agroforestry systems. 2016 June, v. 90, no. 3

2016

Abstract: Managing agricultural land for carbon sequestration becomes more important with rising needs for greenhouse gas mitigation measures. Woodland establishment in upland grasslands can be a carbon sink, but soil carbon losses have also been observed. ... ...

Abstract	Managing agricultural land for carbon sequestration becomes more important with rising needs for greenhouse gas mitigation measures. Woodland establishment in upland grasslands can be a carbon sink, but soil carbon losses have also been observed. Dedicated woodland plots and silvopasture are two contrasting strategies to achieve increased carbon stocks. We compared the carbon sequestration potential of the two approaches with three tree species (Hybrid Larch, Scots Pine and Sycamore) planted on permanent pasture on an upland farm in North East Scotland, 24Â years after planting. Soil organic carbon was measured in the A (
Keywords	B horizons ; Pinus sylvestris ; allometry ; biomass ; carbon ; carbon sequestration ; carbon sinks ; equations ; farms ; grasslands ; greenhouse gases ; highlands ; hybrids ; land management ; pastures ; planting ; silvopastoral systems ; soil organic carbon ; trees ; woodlands ; Scotland
Language	English
Dates of publication	2016-06
Size	p. 371-383.
Publishing place	Springer Netherlands
Document type	Article
ZDB-ID	406958-4
ISSN	1572-9680 ; 0167-4366
ISSN (online)	1572-9680
ISSN	0167-4366
DOI	10.1007/s10457-015-9860-4
Database	NAL-Catalogue (AGRICOLA)

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Article: Effects of manure and mineral fertilization strategies on soil antibiotic resistance gene levels and microbial community in a paddy–upland rotation system

Lin, Hui / Jianrong Fu / Junwei Ma / Stephen J. Chapman / Thomas E. Freitag / Wanchun Sun / Xin Zhang / Zulin Zhang

Environmental pollution. 2016 Apr., v. 211

2016

Abstract: This work investigated the responses of antibiotic resistance genes (ARGs) and the soil microbial community in a paddy–upland rotation system to mineral fertilizer (NPK) and different application dosages of manure combined with NPK. The occurrence of ... ...

Abstract	This work investigated the responses of antibiotic resistance genes (ARGs) and the soil microbial community in a paddy–upland rotation system to mineral fertilizer (NPK) and different application dosages of manure combined with NPK. The occurrence of five tetracycline ARGs (tetA, tetB, tetC, tetG and tetW), two sulfonamide ARGs (sul1 and sul2) and one genetic element (IntI1) was quantified. NPK application showed only slight or no impact on soil ARGs abundances compared with the control without fertilizer. Soil ARGs abundances could be increased by manure-NPK application but was related to manure dosage (2250–9000 kg ha−1). Principal component analysis (PCA) showed that the soil ARG profile of the treatment with 9000 kg ha−1 manure separated clearly from the other treatments; the ARGs that contributed most to the discrimination of this treatment were tetA, tetG, tetW, sul1, sul2 and IntI1. Community level physiological profile (CLPP) analysis showed that increasing manure dosage from 4500 kg ha−1 to 9000 kg ha−1 induced a sharp increase in almost all of the detected ARGs but would not change the microbial community at large. However, 9000 kg ha−1 manure application produced a decline in soil microbial activity. Determination of antibiotics and heavy metals in soils suggested that the observed bloom of soil ARGs might associate closely with the accumulation of copper and zinc in soil.
Keywords	antibiotic resistance genes ; copper ; fertilizer application ; heavy metals ; manure spreading ; microbial activity ; microbial communities ; mineral fertilizers ; NPK fertilizers ; principal component analysis ; soil ; soil microorganisms ; tetracycline ; zinc
Language	English
Dates of publication	2016-04
Size	p. 332-337.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	280652-6
ISSN	1873-6424 ; 0013-9327 ; 0269-7491
ISSN (online)	1873-6424
ISSN	0013-9327 ; 0269-7491
DOI	10.1016/j.envpol.2016.01.007
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Social media and internet driven study recruitment

Chetan Khatri / Stephen J Chapman / James Glasbey / Michael Kelly / Dmitri Nepogodiev / Aneel Bhangu / J Edward Fitzgerald / STARSurg Committee

PLoS ONE, Vol 10, Iss 3, p e

evaluating a new model for promoting collaborator engagement and participation.

2015 Volume 0118899

Abstract: Aims A substantial challenge facing multicentre audit and research projects is timely recruitment of collaborators and their study centres. Cost-effective strategies are required and fee-free social media has previously been identified as a potential ... ...

Abstract	Aims A substantial challenge facing multicentre audit and research projects is timely recruitment of collaborators and their study centres. Cost-effective strategies are required and fee-free social media has previously been identified as a potential conduit. We investigated and evaluated the effectiveness of a novel multi-format social media and Internet strategy for targeted recruitment to a national multicentre cohort study. Methods Interventions involved a new Twitter account, including weekly live question-and-answer sessions, a new Facebook group page, online YouTube presentations and an information page on a national association website. Link tracking analysis was undertaken using Google Analytics, which was then related to subsequent registration. Social influence was calculated using the proprietary Klout score. Results Internet traffic analysis identified a total of 1562 unique registration site views, of which 285 originated from social media (18.2%). Some 528 unique registrations were received, with 96 via social media platforms (18.2%). Traffic source analysis identified a separate national association webpage as resulting in the majority of registration page views (15.8%), followed by Facebook (11.9%), Twitter (4.8%) and YouTube (1.5%). A combination of publicity through Facebook, Twitter and the dedicated national association webpage contributed to the greatest rise in registration traffic and accounted for 312 (48%) of the total registrations within a 2-week period. A Twitter 'social influence' (Klout) score of 42/100 was obtained during this period. Conclusions Targeted social media substantially aided study dissemination and collaborator recruitment. It acted as an adjunct to traditional methods, accounting for 18.2% of collaborator registration in a short time period with no associated financial costs. We provide a practical model for designing future recruitment campaigns, and recommend Facebook, Twitter and targeted websites as the most effective adjuncts for maximising cost-effective study ...
Keywords	Medicine ; R ; Science ; Q
Subject code	360 ; 070
Language	English
Publishing date	2015-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Rare variants in MYD88, IRAK4 and IKBKG and susceptibility to invasive pneumococcal disease

Magda K Ellis / Katherine S Elliott / Anna Rautanen / Derrick W Crook / Adrian V S Hill / Stephen J Chapman

PLoS ONE, Vol 10, Iss 4, p e

a population-based case-control study.

2015 Volume 0123532

Abstract: Although rare variants within the Toll-like receptor signalling pathway genes have been found to underlie human primary immunodeficiencies associated with selective predisposition to invasive pneumococcal disease (IPD), the contribution of variants in ... ...

Abstract	Although rare variants within the Toll-like receptor signalling pathway genes have been found to underlie human primary immunodeficiencies associated with selective predisposition to invasive pneumococcal disease (IPD), the contribution of variants in these genes to IPD susceptibility at the population level remains unknown. Complete re-sequencing of IRAK4, MYD88 and IKBKG genes was undertaken in 164 IPD cases from the UK and 164 geographically-matched population-based controls. 233 single-nucleotide variants (SNVs) were identified, of which ten were in coding regions. Four rare coding variants were predicted to be deleterious, two variants in MYD88 and two in IRAK4. The predicted deleterious variants in MYD88 were observed as two heterozygote cases but not seen in controls. Frequencies of predicted deleterious IRAK4 SNVs were the same in cases and controls. Our findings suggest that rare, functional variants in MYD88, IRAK4 or IKBKG do not significantly contribute to IPD susceptibility in adults at the population level.
Keywords	Medicine ; R ; Science ; Q
Subject code	572
Language	English
Publishing date	2015-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Ability of procalcitonin to discriminate infection from non-infective inflammation using two pleural disease settings.

Fiona J McCann / Stephen J Chapman / Wai Cho Yu / Nick A Maskell / Robert J O Davies / Y C Gary Lee

PLoS ONE, Vol 7, Iss 12, p e

2012 Volume 49894

Abstract: Procalcitonin has been shown to be useful in separating infection from non-infective disorders. However, infection is often paralleled by tissue inflammation. Most studies supporting the use of procalcitonin were confounded by more significant ... ...

Abstract	Procalcitonin has been shown to be useful in separating infection from non-infective disorders. However, infection is often paralleled by tissue inflammation. Most studies supporting the use of procalcitonin were confounded by more significant inflammation in the infection group. Few studies have examined the usefulness of procalcitonin when adjusted for inflammation.Pleural inflammation underlies the development of most exudative effusions including pleural infection and malignancy. Pleurodesis, often used to treat effusions, involves provocation of intense aseptic pleural inflammation. We conducted a two-part proof-of-concept study to test the specificity of procalcitonin in differentiating infection using cohorts of patients with pleural effusions of infective and non-infective etiologies, as well as subjects undergoing pleurodesis.We measured the blood procalcitonin level (i) in 248 patients with pleural infection or with non-infective pleural inflammation, matched for severity of systemic inflammation by C-reactive protein (CRP), age and gender; and (ii) in patients before and 24-48 hours after induction of non-infective pleural inflammation (from talc pleurodesis).1) Procalcitonin was significantly higher in patients with pleural infection compared with controls with non-infective effusions (n = 32 each group) that were case-matched for systemic inflammation as measured by CRP [median (25-75%IQR): 0.58 (0.35-1.50) vs 0.34 (0.31-0.42) µg/L respectively, p = 0.003]. 2) Talc pleurodesis provoked intense systemic inflammation, and raised serum CRP by 360% over baseline. However procalcitonin remained relatively unaffected (21% rise). 3) Procalcitonin and CRP levels did not correlate. In 214 patients with pleural infection, procalcitonin levels did not predict the survival or need for surgical intervention.Using a pleural model, this proof-of-principle study confirmed that procalcitonin is a biomarker specific for infection and is not affected by non-infective inflammation. Procalcitonin is superior to CRP in distinguishing infection from non-infective pleural diseases, even when controlled for the level of systemic inflammation.
Keywords	Medicine ; R ; Science ; Q
Subject code	610 ; 616
Language	English
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Risk of nontyphoidal Salmonella bacteraemia in African children is modified by STAT4

Nature Communications, Vol 9, Iss 1, Pp 1-

2018 Volume 11

Abstract: Nontyphoidal Salmonella (NTS) is a major cause of bacteraemia in children and HIV-infected adults in Africa. Here, Gilchrist et al. conduct a genome-wide association study and show that genetic variation in STAT4 is a determinant of NTS in Kenyan and ... ...

Abstract	Nontyphoidal Salmonella (NTS) is a major cause of bacteraemia in children and HIV-infected adults in Africa. Here, Gilchrist et al. conduct a genome-wide association study and show that genetic variation in STAT4 is a determinant of NTS in Kenyan and Malawian children.
Keywords	Science ; Q
Language	English
Publishing date	2018-03-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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