Tag Archives: Online First

Differences in gut microbiota and serum Trimethylamine N-oxide (TMAO) levels in patients with colorectal cancer with a small, nested case-control study

Jian Huang1, Xiaohua Chen1, Qinglian Zhong1*

[1] Department of Gastroenterology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong 518033, China


The dysbiosis of the gut microbiota caused by drug metabolism and diets may influence the gastrointestinal (GI) barrier and their ability for normal attachment and further immunity system, which all could be associated with the medical efficacy of colorectal cancer (CRC) during chemotherapy.

This study aims to investigate Trimethylamine N-oxide (TMAO), a gastrointestinal product readily entering the bloodstream, as a potential risk factor for various diseases, including CRC.

To investigate the relationship between gut microbiota dysbiosis and carcinogenesis in CRC patients, we analyzed taxonomic alterations in the gut microbiota of 77 subjects, including 36 CRC patients and 41 normal controls. We collected samples of the participants’ microbiome from their fecal material and utilized 16S rRNA sequencing to identify the microbial composition. Additionally, to predict the functions of the GI microbiota, Phylogenetic Investigation of Communities by Reconstructing Unobserved States (PICRUSt) was employed. This could serve as a promising biomarker for colorectal cancer. Moreover, the serum level of TMAO between the CRC and healthy controls was also compared, and it was observed that the intestinal microbiome was changed in CRC patients; however, the serum level of TMAO was not correlated with the progression of CRC.

In conclusion, in the present study, instead of relying solely on TMAO, which is a convenient clinical test, we focused on the treatment of CRC by emphasizing the modification of the intestinal microbiome.

Keywords: CRC, Intestinal microbiome, TMAO, 16s rRNA, PICRUSt

Comparative assessment of β-propiolactone, binary ethyleneimine and formaldehyde in inactivating Foot and Mouth Disease virus serotype O

Muhammad Amjad Iqbal1, 2, Noreen Sarwar1*, Sohail Raza1, Sehrish Firyal3, Rabia Riaz4, Afia Muhammad Akram5, Rashad Munir4, Aamir Riaz Khan4, Mobeen Sarwar6, Muhammad Imran Arshad7

1Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan

2Veterinary Research Institute, Lahore, Pakistan

3Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan

4Foot and Mouth Disease Research Centre, Lahore, Pakistan

5Department of Zoology, Division of Science and Technology, University of Education, Lahore, Pakistan

6Livestock and Dairy Development, Government of Punjab, Lahore, Pakistan

7Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan


Inactivation of foot-and-mouth disease virus (FMDV) with Formalin (FA) and binary ethyleneimine (BEI) is a slow process and takes long time. The purpose of this study was to evaluate β-Propiolactone (BPL), an alkylating agent that is frequently used in vaccine development and production, as a candidate for the inactivation of FMDV serotype O. Virus was grown on confluent monolayer of BHK-21 cell line. Harvesting was performed between 18 and 20 hours after infection, when CPE was between 90 and 95%. The virus was subjected to inactivation with formalin (0.02%), BEI (2mM, 2.5mM, 3mM) and BPL (0.1%, 0.2 and 0.4%) at 4°C and 37°C. Samples (05 mL/each) were collected after 0, 2, 4, 8, 16, and 24 hours post treatment. The biological titer (TCID50/ml) of each inactivated sample was measured. An innocuity test was used to further confirm the inactivation. RT-PCR was used to detect viral genome damage by amplification of VP1 gene. Data were analyzed by one-way analysis of variance and pair wise comparison was made by post hoc Tukey’s HSD test. Linear regression was used in Microsoft Excel Version 2010. The virus titers after 0.02% formalin treatment were 7.172±0.298 and 4.584±1.362 at 4°C and 37°C respectively. The virus titers were 6.036±0.513, 5.622±0.298, and 5.150±0.449 with 2mM, 2.5mM, 3mM BEI at 4°C and 1.646±1.0210, 1.050±0.644, 0.492±0.492 at 37°C respectively. Inactivation with 0.1%, 0.2% and 0.4% BPL at 4°C resulted in virus titers of 2.386±1.1104, 1.4400±0.9445 and 0.6960±0.6960 respectively. Rapid inactivation of virus with all three BPL concentrations at 37°C gave mean titer of 0.00±0.00. There was a significant difference (P<0.05) among all treatment groups with highest inactivation rates recorded for BPL.

Keywords: FMDV, BHK-21, Inactivation, BEI, BPL, Formalin

Habitat modelling of Bombus haemorrhoidalis Smith (Hymenoptera) under future projected climatic conditions in Pakistan

Imran Bodlah1*, Ammara Gull E Fareen2, Umer Ayyaz Aslam Sheikh3, Muhammad Adnan Bodlah4, Rehana Bibi5, Hesham F. Alharby6, 7, Habeeb M. Al-Solami6, Naser A. Alkenani6, Abdullah G. Al-Ghamdi6

1Insect Biodiversity and Conservation Group, Department of Entomology, PMAS Arid Agriculture University, Rawalpindi, Pakistan

2Department of Environmental Sciences, PMAS Arid Agriculture University, Rawalpindi, Pakistan

3Department of Entomology, University of Poonch, Rawalakot, Azad Jammu and Kashmir, Pakistan

4Fareed Biodiversity Conservation Centre, Department of Agricultural Engineering, Khawaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Punjab, Pakistan
5Department of Plant Protection, Faculty of Agricultural Sciences, Ghazi University D. G. Khan

6Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia

7Plant Biology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia


Bumble bees are among the insects that play a significant role in the pollination of several agricultural crops, fruits, vegetables, and wild flowering plants. Climate change has been discussed as a prospective threat to the biodiversity of these pollinators in different parts of the planet during the next several decades. As a result of expected climate change circumstances, a number of studies have determined that the distribution range of bumble bees will alter, with some species becoming extinct and majority of them relocating to the higher mountainous areas. Numerous countries around the globe have developed conservation measures for these ecologically and economically significant organisms. In Pakistan, Bombus haemorrhoidalis (Hymenoptera: Apidae) is more likely to be used as a pollinator in greenhouse vegetable production, as compared to other documented species. Our research aimed to find moderately and highly favorable locations for B. haemorrhoidalis in 2050 and 2070 based on two representative concentration pathways (RCP4.5 and RCP8.5) using Maxent. Five key contributing variables including Bio1 (Annual Mean Temperature), Bio12 (Annual Precipitation), Bio14 (Precipitation of Driest Month) and Bio18 (Precipitation of Warmest Quarter) along with 52 occurrence record of the species were utilized in the modeling procedure for determining potential distribution of B. haemorrhoidalis. Performance of the model was assessed by calculating the area under the curves (AUC), the partial ROC, the omission rates (E=5%), and the AICc (Model complexity). Regularization multiplier of finally selected model was 2. Based on the results of the Jackknife test, it was determined that only four climatic factors, namely Bio4, Bio12, Bio14 and Bio18 contributed 89.0% to the prediction of the species’ prospective distribution. The results indicated that highly suitable distribution areas of this species would be concentrated in upper the mountainous areas of Pakistan under the influence of climate change. The suitability of its habitat, however, will decrease under the forecasted climatic conditions of future scenarios (RCP 4.5 and RCP 8.5) for 2050 and 2070. According to the findings, the area that is anticipated to be moderately suitable will shrink by 320.492083 km2between the years 2050 and 2070 under RCP 4.5 (70), as compared to RCP 4.5. (50). In the same pattern, according to RCP 8.5 (70), it would shrink by a total of 260.764698 km2 as compared to RCP 8.5. (50). A similar pattern would be observed for forecasted highly suitable areas, which would shrink by a total of 2492.820215 km2 under RCP 4.5. (70) compared to RCP 4.5 (50), and by a total of 1363.441658 km2 under RCP 8.5 (70) in contrast to RCP 8.5. (50). Results indicated that suitable areas for this species would decrease during two scenarios of year 2050 and 2070. This species would leave many areas of its current distribution under the influence of climate change and move upward towards upper mountainous areas of Azad Kashmir, Gilgit Baltistan and Khyber Pakhtunkhwa. Based on the results of our studies, Government along with other stakeholders of bee pollination may develop climate mitigation strategies to conserve pollination services of B. haemorrhoidalis on a sustainable basis. More extensive surveys are needed along with other tools of remote sensing for more reliable predictions.

Keywords: Bombus haemorrhoidalis, Habitat suitability, Environmental predictors, Maxent, Climate change, Pakistan

Green synthesis of zinc oxide microparticles using the leaf extract of Dolichandrone spathacea in sustainable agriculture: a new approach for protecting the legume plant (Vigna radiata) against the Cr(VI) stress

Nguyen-Huan Pham-Khanh1, Nhat-Quynh Huynh1, Hong-Ngoc-Bao Le1, Thi-Kim-Quy Ha1*

1College of Natural Sciences, Can Tho University, Campus II, 3/2 street, Ninh Kieu district, Can Tho City 94000, Vietnam


The hazardous heavy metal ion Cr(VI) is harmful and easily mobile in the environment. Cr(VI) poisoning can cause delayed seed germination and damaged plant growth. This study suggested a green and simple synthesis method of ZnO microparticles (ZnO MPs) from Zn(CH3COO)2 solution and aqueous leaf extract of Dolichandrone spathacea (L. f.) K. Schum for protecting the legume plant (Vigna radiata) against the Cr(VI) stress. The optimized conditions for the synthesis of these MPs were determined using computational and experimental approaches. The characterization of ZnO MPs was analyzed by surface morphology, particle sizes, and elemental components using modern methods. The Zn MPs successfully exhibited the potential protective effects on the seed germination and seedling vigor of V. radiata under Cr(VI) stress. The results of PPR and ABTS assays also indicated that the antioxidant capacity of non-enzymatic antioxidants from leaves under Cr(VI) stress significantly reduced (46.83 ± 1.938% and 69.60 ± 2.17%, respectively) as compared to supplement of ZnO-MPs increased (55.44 ± 2.624% and 78.07 ± 0.820%, respectively). This study is an essential report for the agricultural field, which can apply further the new and green zinc-micronutrient fertilizer to mitigate the adverse effects of heavy metal contamination on crop cultivation.

Keywords: Green synthesis, Zinc oxide microparticles, Dolichandrone spathacea, Cr(VI) stress, Vigna radiata.

Isolation, identification and biological characteristics of pathogenic Enterococcus faecalis from Tibetan sheep

Wang Dongjing1*, Su Zhonghua2, Yuan Zhenjie1, Mikhlid H. Almutairi3

1Institute of Animal Husbandry and Veterinary, Tibet Autonomous Regional Academy of Agricultural Sciences, Lhasa 850009, China

2Tibet Autonomous Region Animal Disease prevention and Control Center, Lhasa 850009, China

3Zoology Department, College of Science, King Saud University, P.O. Box: 2455, 11451, Riyadh, Saudi Arabia


This study was conducted to identify the biological characteristics of pathogen responsible for the death of Tibetan sheep in Nagarze County, Tibet, China. For this purpose, samples were collected from diseased animals and for bacterial culture and isolation. The isolated strains were subjected to several tests which included gram staining, biochemical identification, PCR amplification, genetic evolution analysis, in-vitro drug sensitivity and in-vivo pathogenicity tests. The results revealed that 7 strains of gram-positive cocci were isolated from Tibetan sheep, named TS-1, TS-2, TS-3, TS-4, TS-5, TS-6, and TS-7. These strains exhibited specific biochemical characteristics consistent with Enterococcus faecalis. Whereas, PCR amplification results were consistent with the expected outcomes on target band of approximately 1500 bp. Genetic evolutionary analysis revealed a significant homology (96.0%-99.9%) between the isolates and Enterococcus faecium. In-vitro drug sensitivity tests demonstrated that all the isolates exhibiting multiple drug resistance. Furthermore, the isolated strains displayed varying degrees of pathogenicity in mice. This study confirms that Enterococcus faecium is the causative agent for the deaths of Tibetan sheep. These findings enhance our understanding of the disease and suggest valuable insights for its prevention, control, and future research.

Keywords: Tibetan sheep, Enterococcus faecium, Isolation, Identification, Drug resistance, Pathogenicity

Epidemiological investigations of bovine brucellosis and evaluation of loop mediated isothermal amplification assay for field application

Muhammad Bilal1, Shafia Tehseen Gul1*, Muhammad Tariq Javed1, Muhammad Saqib2

1Department of Pathology, Faculty of Veterinary Sciences, University of Agriculture, Faisalabad, Pakistan

2Department of Clinical Medicine and Surgery, Faculty of Veterinary Sciences, University of Agriculture, Faisalabad, Pakistan


Brucellosis is considered as a highly contagious and zoonotic disease globally and various diagnostic tests are available for its diagnosis. Keeping in view, the limitations of currently used serological techniques, a more precise, sensitive, and reliable loop mediated isothermal amplification (LAMP) assay was evaluated as an emerging diagnostic tool. In the current study, serum samples from cows (n=1989) and buffaloes (n=1467) were collected from the study area i.e., District Faisalabad and Toba Tek Singh in Punjab, Pakistan. As these two districts are present around the river Ravi in Punjab, Pakistan and known as the house of Nili Ravi breed. A number of dairy farms of local and imported cows are also present in this area. Initially the samples were screened by the RBPT and then subjected to c-ELISA for confirmation. Overall, 12.16 and 9.3% cows and buffaloes were seropositive through RBPT while 11.21 and 7.70% cows and buffaloes were seropositive via c-ELISA. The positive samples from c-ELISA were further subjected to molecular amplification at 1.5% agarose gel through LAMP assay. The current study concludes that LAMP assay is more sensitive as compared to other conventional PCR techniques while detecting true positives for brucellosis, so it can be used for confirmation of Brucella abortus as compared to PCR. In addition to the sensitivity and specificity and qualitative results can be observed through naked eye in LAMP, which is not possible in PCR.

Keywords: Brucellosis, LAMP, Quick diagnosis, Serological techniques, Rapid point of care

DNA barcoding reveals arthropod diversity and unveils seasonal patterns of variation in Quetta region, Pakistan

Hina Ali Ahmed1, Nazeer Ahmed2, Shahjahan Shabbir Ahmed2, Shagufta Saddozai1, Afroz Rais3,

Imran Ali Sani2, Dawood Shahid2, Shahbaz Khan4*

1Department of Zoology, Sardar Bahadur Khan Women’s University, Quetta, Pakistan

2Department of Biotechnology, Faculty of Life Sciences, BUITEMS, Quetta, Pakistan

3Department of Botany, Sardar Bahadur Khan Women’s University, Quetta, Pakistan

4Colorado Water Center, Colorado State University, Fort Collins, Colorado 80523, USA


Deoxyribonucleic acid (DNA) sequencing is an emerging approach for revealing species diversity that has made species identification possible. This technique is an amazing and useful tool for studies in taxonomy, evolutionary biology, and biodiversity. Sequences of DNA can be used as genetic “barcodes” which could be used to  identify all animals, including insects. True flies, belonging to the order Diptera, are widely distributed and crucial components of ecosystems worldwide. Despite the rich biodiversity of Pakistan, our knowledge of various insect groups particularly flies remains limited. The current study was conducted in Quetta, Pakistan, from June 2017 to May 2018, to use DNA barcoding technique for the determination of the diversity of flies (658 bp sequence from the 5′-end of cytochrome oxidase I). Our analysis focused on a specific region of the cytochrome c oxidase 1 (COI) gene, known as the barcode region which provides valuable information for inferring evolutionary relationships and identifying species. The obtained sequences of 2,195 fly specimens were then compared and matched against the Barcode of Life Data System (BOLD), which assigned the specimens to 309 Barcode Index Numbers (BINs), which operates as a counterpart in the BOLD database. Among the families identified, Muscidae was the most dominant, with 283 specimens, followed by Cecidomyiidae with 184 specimens, and Ceratopogonidae with 164 specimens. A total 82 number of species were identified with Tricimba humeralis with the maximum catch.

Keywords: Arthropod, BOLD, Barcode index number, Biodiversity, Cytochrome c oxidase I, DNA barcoding

Isolation and Molecular Identification of Serratia Nematodiphila associated with Red Palm Weevil, Rhynchophorus Olivier (Coleoptera: Curculionidae) as bio-insecticide in Egypt

Mahmoud Abbas Ali1, Mervat A. B. Mahmoud2, Muhammad Shoaib3, Zeeshan Ahmad Bhutta4*, Nada M. Ali5, Nadeem Ali6, Hani Z. Asfour7, Nisreen Rajeh8, Mohamed R. Eletmany9,10

1Department of Plant Protection, Faculty of Agriculture, South Valley University, Qena, Egypt

2Department of Zoology, Faculty of Science, South Valley University, Qena, Egypt

3Key Laboratory of New Animal Drug Project, Gansu Province/Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs/Lanzhou Institute of Husbandry and Pharmaceutical Sciences of the Chinese Academy of Agricultural Sciences, Lanzhou 730050, China

4Laboratory of Veterinary Immunology and Biochemistry, College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea

5Department of Chemistry, Faculty of Science, Al-Baha University, Al-Baha 65799,  Saudi Arabia

6Center of Excellence in Environmental Studies, King Abdulaziz University, Jeddah, 21589, Saudi Arabia

7Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia

8Department of Clinical Anatomy, Faculty of Medicine, King Abdulaziz University, Jeddah, 21589, Saudi Arabia

9Department of Chemistry, Faculty of Science, South Valley University, Qena, Egypt

10TECS Department, Wilson College of Textiles, NC State University, Raleigh 27606, USA


The red palm weevil (RPW), Rhynchophorus ferrugineus Olivier (Coleoptera: Curculionidae) is a major date palm pest. In this study, we aimed to isolate and identify the Serratia nematodiphila from RPW as potential biocontrol agents. We isolated the bacteria from infected RPW larvae and adults and identified using colony morphology characteristics, biochemical tests, and PCR followed by 16S rRNA sequencing. This is the first study reporting the Serratia nematodiphila as an extracellular symbiont of RPW from Egypt. The potential of this bacteria to be used as biocontrol agent was conducted by a screening bioassay through its effect on RPW eggs. The study noted that treated eggs were unable to hatch and not turned red in color, indicating the potential of this bacteria to be used as bio-pesticide. These results presented novel insights into the microbiome of RPW and suggest the potential of Serratia nematodiphila as a biocontrol agent for RPW management. Moreover, further studies are required to explore the mechanism and potential of these bacteria in field applications. Nevertheless, this study provides a promising direction for the development of sustainable and environmentally friendly RPW management strategies.

Keywords: Red Palm Weevils (RPW), Rhynchophorus ferrugineus, Coleoptera, Curculionidae, Serratia nematodiphila, Biocontrol agent

Analysis of the azoreductase gene harbored by Alcaligenes sp. YB4 capable of concurrent removal of sulphonated azo dye and hexavalent chromium

Yasir Bilal1, Sabir Hussain1*, Muhammad Shahid2, Tanvir Shahzad1, Faisal Mahmood1

1Department of Environmental Sciences, Government College University Faisalabad, Pakistan.

2Department of Bioinformatics & Biotechnology, Government College University Faisalabad, Pakistan


Continuous discharge of textile wastewater consisting of variety of pollutants is a serious threat to ecosystems. Microbial bioremediation might serve as an effective approach for treating these unwanted contaminants. In this study, several bacteria isolated from textile wastewater were studied for decolorization of Congo red (CR) dye. The strain Alcaligenes sp. YB4 showed the most efficient potential to decolorize CR dye. Moreover, this strain efficiently decolorized CR while concurrently removing hexavalent chromium [Cr(VI)] in the same medium with maximum removal (> 90 %) of both pollutants at pH 7 and pH 8. The potential of YB4 for concurrent removal of both pollutants was observed to decrease with increasing concentration of NaCl. Similarly, Alcaligenes sp. YB4 efficiently removed the 91.6 % of CR and 95.7 % of Cr(VI) simultaneously, under static condition as compared to the shaking condition. While MS media amended with yeast extract showed about 92.2 % and 90.1 % removal of CR and Cr (VI) within 48 hours of incubation, respectively. Moreover, it was also noticed that presence of heavy metals effected the concurrent removal of both pollutants. The in-silico analysis of the azoreductase amplified from the strain YB4 identified the binding of CR with azoreductase and proposed the hypothesis that their association may be the primary cause of CR degradation. This study indicated that Alcaligenes sp. YB4, having azoreductase gene, is a potential resource to treat textile wastewater.

 Keywords: Congo red, Hexavalent chromium, Azoreductase, Molecular docking, Azo dyes

Nitrogen management in a sandy loam soil grown with cucumber plants and fertilized by vermicompost

Khaled Mohamed Lela, Abdellatif Saleh El-Sebaay, Shaimaa Hassan Abd-Elrahman*, Mahmoud Mohamed Elbordiny

Soil and Water Department, Faculty of Agriculture, Ain Shams University, P.O. Box 68–Hadayek Shoubra, Cairo 11241, Egypt


Global attention is shifting to using fertilizers organically produced from available wastes in the surrounding ecosystem to provide sustainability in agriculture and conserve the environment. The aim of this study is to investigate the possible changes in the yield and quality of cucumber resulting from different combinations of organic solid and liquid fertilizers prepared from different organic wastes, as compared to applying mineral fertilizers. Furthermore, detecting available N concentration in sandy loam soil and total N concentration in cucumber leaves considering the effect of the studied treatments every 15 days after transplanting (DAT) until 120 DAT. Four fertilizer treatments (3 organic fertilizers, i.e., vermicompost (VC), pigeon manure (PM), and compost (COMP) in addition to mineral fertilizers) were tested in a randomized complete blocks design with three replicates. The organic fertilizer treatments were divided into three categories, the first was solid added through two equal doses. The second category was like the first one plus adding vermicompost tea (VCT) through drip irrigation (DI). The third category was like the second one, but the VCT was substituted with pigeon manure tea (PMT). Obtained results showed that the treatments of PM50/50, and VC50/50 as ground applications plus PMT or VCT through DI were given significant increases in available N in the studied soil, and enhanced the cucumber plant growth parameters, yield traits, and the total concentration of N in leaves throughout the experimental period. Additionally, the highest benefit/cost ratio (5.68) was achieved with the application of organic treatments compared to traditional ones (3.28).

Keywords: Vermicompost, Pigeon manure, Organic aqueous extract, Organic farming, Detecting N in soil and plant, Cucumber plants