Muhammad Hammad Zafar

Dr. Muhammad Hammad Zafar

orcid

Research Focus & Metrics

Academic Career Length

7Years (2020-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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29 October 2025 in Animals
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Journal Article
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SESalwa Eman
Salwa Eman
RDRaza Mohai Ud Din
Raza Mohai Ud Din
MZMuhammad Hammad Zafar
Muhammad Hammad Zafar
MZMengke Zhang
Mengke Zhang
XWXin Wen
Xin Wen
XGXiaodong Guo
Xiaodong Guo
Animal diseases remain a major constraint to livestock productivity and public health, necessitating accurate, early diagnostic methods. This review examines the classification and mechanisms of diagnostic, prognostic, and predictive biomarkers in veterinary medicine and evaluates how advanced technologies enable their discovery. Mechanistically, biomarkers function as molecular indicators of disease presence, progression, or therapeutic response, and are essential in species where clinical signs often appear late or are non-specific. We detail the contribution of high-throughput omics platforms, genomics (NGS, RNA-Seq), proteomics (LC-MS/MS, DIGE), and metabolomics (NMR, LC-MS/MS) in identifying disease-specific molecular signatures. Emerging technologies, including CRISPR/Cas9, AI-enhanced imaging, aptamer-based biosensors, and microfluidic devices, show significant diagnostic potential. Case studies, including canine melanoma, bovine respiratory disease complex (BRDC), and congenital portosystemic shunts in dogs, illustrate the real-world applicability of biomarkers. Challenges such as a lack of standardization, species variability, and poor clinical translation are acknowledged. The review concludes that integrating biomarker mechanisms with advanced analytical technologies is key to advancing veterinary diagnostics and disease control.

2 July 2025 in Microorganisms
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MMMaida Mushtaq
Maida Mushtaq
XNXiaojun Ni
Xiaojun Ni
Muhammad KhanMuhammad Khan
Muhammad Khan
XZXiaoqi Zhao
Xiaoqi Zhao
HYHongyuan Yang
Hongyuan Yang
GQGuobo Quan
Guobo Quan
Dietary protein levels greatly influence gut microbial ecosystems; however, their effects on gut archaea and associated functions in ruminants require further elucidation. This study evaluated the impact of varying dietary protein levels on gut archaeal composition, antimicrobial resistance (AMR) genes, virulence factors, and functional capacities in sheep. Eighteen ewes (Yunnan semi-fine wool breed, uniparous, 2 years old, and averaging 50 ± 2 kg body weight) were randomly assigned to diets containing an 8.5 (low; H_1), 10.3 (medium; H_m), or 13.9% (high; H_h) crude protein level from the 35th day of pregnancy to the 90th day postpartum. The total duration of the experiment was approximately 202 days. A total of nine fecal samples (three from each group) were analyzed via 16S rRNA and metagenomics sequencing. Higher archaeal alpha diversity and richness were observed in the H_m and H_h groups compared to the H_l group (p < 0.05). A Beta diversity analysis revealed the archaeal community’s distinct clustering mode based on protein levels. The methanogenic genera Methanobrevibacter and Methanocorpusculum were dominant across the three groups, and their abundance was influenced by protein intake. A functional prediction analysis indicated moderate changes in amino acid and carbohydrate metabolism, which are particularly associated with methane production, an important source of greenhouse gases. AMR genes (e.g., tetA (60), patA, vat, and Erm methyltransferase) and virulence factors (Bacillibactin, LPS) were significantly enriched when animals were fed high-protein diets. Our results demonstrated that dietary protein levels significantly influence gut archaeal composition, AMR gene enrichment, and related functional pathways. Medium-protein diets promoted greater archaeal diversity, whereas high-protein diets favored resistance gene proliferation and enhanced methanogenic activity. Optimizing dietary protein intake may enhance gut health, mitigate antimicrobial resistance risk, and reduce methane emissions, thereby supporting livestock sustainability and environmental protection.

26 April 2024 in Fermentation
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CLChuang Li
Chuang Li
ZLZhiqi Lu
Zhiqi Lu
RQRuxin Qi
Ruxin Qi
Zhenbin ZhangZhenbin Zhang
Zhenbin Zhang
YLYue Lu
Yue Lu
Mengzhi WangMengzhi Wang
Mengzhi Wang
Silage is the most important component of a ruminant diet and has important production and health significance in ruminant production. The aim of the research was to investigate how the mixed silage of Chinese cabbage waste and rice straw (mixed silage) impacts the fecal microorganisms and metabolites in Hu sheep using Illumina sequencing and metabolomic analysis. A total of 16 Hu sheep (8 rams and 8 ewes) weighing about 39 kg and 5.5 months old were used as experimental sheep and divided into two groups (4 rams and 4 ewes, n = 8) using the principle of randomized trials: the control group with peanut sprouts, corn husks, and sorghum husks as roughage and the silage group with the mixed silage as roughage. There were no significant differences in the average daily gain (ADG), dry matter intake (DMI), or feed conversion rate (FCR) between the control group and the mixed silage groups (p > 0.05). Microbiome results showed that 15 microorganisms such as Ruminococcaceae UCG 010, Breznakia, Erysipelothrix, Desulfovibrio, Succiniclasticum, and Shuttleworthia were significantly different between the two groups. In addition, metabolomics showed that the mixed silage modulated the concentrations and metabolic pathways of metabolites in the manure. Significantly different metabolites were mainly enriched in amino acid anabolism (“glycine, serine, and threonine metabolism”, “valine, leucine, and isoleucine biosynthesis”, “arginine biosynthesis”, etc.), nucleic acid metabolism (pyrimidine metabolism). In conclusion, the addition of mixed silage to the diet of Hu sheep can alter the structure of the hindgut microflora and regulate the metabolism of amino acids and nucleotides, which affects health performance.

28 June 2023 in Pakistan Journal of Biotechnology
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AKAbdul Khaliq
Abdul Khaliq
MZMuhammad Hammad Zafar
Muhammad Hammad Zafar
Muhammad SajjadMuhammad Sajjad
Muhammad Sajjad
MHMahmood-Ul Hassan
Mahmood-Ul Hassan
MMMuhammad Akhlaq Mudassar
Muhammad Akhlaq Mudassar
SNSalma Niaz
Salma Niaz
Low nitrogen fertilizer use efficiency and high losses of nitrogen are the critical challenges being faced by sunflower grower. To address these concerns, an experiment was carried out during spring 2021 at the Agronomic research area of the Agriculture University, Faisalabad. The randomized complete block design experiment was used with three replications under split plot arrangement. The 5m x 3m net plot size was kept with sowing procedures retained in the main plot and nitrogen application techniques kept in the sub plot. The experiment was planted on 20-02-2021. The matured crop was reaped on 18 June, 2021 manually. The single row hand drill was used to sow sunflower crop. The 75 cm line to line and 25 cm plant to plant distance was maintained. The results indicated that plant population ranged from 73 to 74 with maximum plant height of 174.33 cm, stem diameter (3.70 cm), head diameter (23.13 cm), number of achenes per head (1237.6), 1000-achene weight (68.17 g), highest biological yield (10.92 t ha-1), achene yield (3.22 t ha-1), harvest index (29.48 %) and protein contents (29.03 %) was observed in treatment where nitrogen was applied by fertigation method and sunflower was sown on beds. But maximum oil contents (41.78 %) were observed where nitrogen was side dressed and flat sowing technique was adopted for crop sowing. It is found that use of fertigation method of nitrogen application and bed planting techniques proved to be the best combination for improving growth, yield & yield relating attributes and improve fertilizer use efficiency with lower nitrogen losses for sunflower (Hybrid-33) under agro-climatic conditions of Faisalabad.

8 January 2024 in Fermentation
Verified
Journal Article
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ZLZhiqi Lu
Zhiqi Lu
CLChuang Li
Chuang Li
LHLie Hou
Lie Hou
Zhenbin ZhangZhenbin Zhang
Zhenbin Zhang
YLYue Lu
Yue Lu
Mengzhi WangMengzhi Wang
Mengzhi Wang
Improper disposal of vegetable waste can cause serious environmental pollution, but because they contain huge water content and organic matter, they are not suitable for disposal by methods such as incineration and landfill. However, vegetable waste contains a large amount of nutrients and have some complementary effects with rice straw in terms of physical structure, nutrients, and moisture. In this experiment, the plant feed (corn husk, peanut shells and sorghum shells) was used as the control group (CON group), and the mixed silage of Chinese cabbage waste and rice straw (mixed silage) was used as the experiment group (TRE group), and its safety performance was evaluated by testing its toxin content, pesticide residues, vitamin contents and feeding experiment of Hu sheep. In the animal experiment, 16 healthy Hu sheep (5.5 months, 39.11 ± 4.16 kg) were randomly divided into two groups of 8 each. The results of the safety performance evaluation showed that the content of mycotoxins, heavy metals, and nitrites as well as pesticide residues in the crude feeds of both groups were within the range of Chinese feed hygiene standards. In addition, the levels of deoxynivalenol (DON) and aflatoxin (AFT) in the CON group were lower, while the content of ochratoxin (OTA) and zearalenone were higher than those in the TRE group (p < 0.05). The levels of plumbum(Pb), chromium (Cr), cadmium (Cd), and nitrite in the CON group were lower than the mixed silage, while the levels of As were higher than the mixed silage (p < 0.05). It is worth noticing that the content of vitamin B2 (VB2) and vitamin C (VC) in the TRE group was higher than the CON group (p < 0.05). The results of the feeding experiment showed that the mixed silage did not affect the growth performance, nutrient digestibility, organ index, and intestinal index of Hu sheep (p > 0.05). In addition, the mixed silage reduced the weight of omasum, the proportion of omasum to live weight before slaughter, the amount of compound stomach, and the proportion of compound stomach to live weight before slaughter, which were higher than those in the TRE group (p < 0.05). The thickness of the basal layer of the rumen abdominal sac, the red blood cell count, the content of IL-10, and TNF-α in the blood, and TNF-α content in the rumen of the Hu sheep in the TRE group were higher than the CON group (p < 0.05). In conclusion, the feed safety index content of the mixed silage did not exceed the Chinese feed hygiene and safety standards and did not cause adverse effects on the growth performance of the Hu sheep, and it improved the immune performance of the body and digestive tract of the sheep to a certain extent and promoted the healthy development of the sheep.

1 January 2020 in Anais da Academia Brasileira de Ciências
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Journal Article
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MSMuhammad Sharif
Muhammad Sharif
MZMuhammad Hammad Zafar
Muhammad Hammad Zafar
SRSajjad Ur. Rahman
Sajjad Ur. Rahman
SASidra Anam
Sidra Anam
KAKhurram Ashfaq
Khurram Ashfaq
DADr Amjad Islam Aqib
Dr Amjad Islam Aqib
Biomass of Saccharomyces cerevisiae wasenhancedin rice polishing by fermentation to increase protein contents of feedfor its use in livestock. Broth culture of Saccharomyces cerevisiae (2.6×108CFU/mL) was prepared from culture obtained by continuous streaking. The isolated culture was identified morphologically by Gram staining and confirmed by biochemical characteristics. Rice polishing was sieved to remove larger particles. Then it was distributed to 4 treatments in triplicates. Treatments were represented as rice polishing (RP), rice polishing plus Saccharomyces culture (RPSC), rice polishing plus ammonium sulphate (RPAS), rice polishing plus Saccharomyces culture plus ammonium sulphate (RPSCAS).Fermentation was provided for 144 hours at 320C,while samples were collected after every 24 hours. Samples were dried, ground and subjected to proximate analysis. It was observed that protein content was increased from 11% to 21.51% and maximum increment was obtained after 144 hours of incubation in RPSC treatment. Ether extract and ash were increased from 14% and 10% to 16.96% and 11.11% in RPSCAS respectively. A significant reduction in neutral detergent fiber was observed after fermentation. It is concluded that Saccharomyces cerevisiae has potential to improve mineral and protein contents of rice polishing by fermentation process with or without addition of nitrogen source.