A 27 days experiment was performed in February 2019 at the Center for livestock production (SHF, NMBU, Ås, Norway), which is an animal experimental unit approved by the National Animal Research Authority (permit no. 174). All pigs were handled under the applicable laws and regulations controlling experiments with live animals in Norway (regulated by the “Animal Welfare Act” and “The Norwegian Regulation on Animal Experimentation” derived from the “Directive 2010/63/EU on the protection of animals used for scientific purposes.
Animals and Housing
Eighty crossbred [Norwegian Landrace x Yorkshire z-line) x Duroc)] weanling pigs, selected from eleven litters (four or eight pigs from each litter) were included in the experiment. Pigs who had been under medical treatment in the nursing period were excluded. All piglets had access to the sows feed during the nursing period. The average weaning age was 32.8 ± 1.6 SD days and the average weaning weight 10.6 ± 0.8 SD kg. Pigs were blocked by litter, weight, and sex and assigned to one of four dietary treatments. Pigs were distributed in pens of four, and from a total of five pens per treatment, three of the pens per treatment were installed with rubber mats. The remaining pens had access to wood shavings as bedding material. The pen size was 1.6 m2. The room temperature was logged every morning, and the average temperature for the experimental period was 21.6 ± 1.4 °C.
Dietary treatments
BSFL meal was produced at HiProMine S.A., Poznan, Poland. The BSFL feed was normalized in terms of dry matter (DM) content by the addition of wheat middlings (17%) to fresh vegetables and fruit mix, consisting of apples (15%) carrots (50%) potatoes (15%) and cabbage (20%) and established at the level of 22% DM. Fresh vegetable pre-consumer waste was ground (2000 rpm/1 min, (HPM milling system, 55 kW, Poland) to pass a 2 mm screen and offered ad libitum to the BSFL. Substrates were not contaminated by any animal products in accordance with EC regulation (no 1069/09). At the prepupal stage (10th day of rearing), larvae were harvested, sieved through a 3 mm screen, and washed with water on drum separator at 90 ⁰C for 10 minutes (HPM cleaning system, Poland).
The dietary treatments included a control diet and three experimental diets with increased inclusion of BSFL; 4.76% (BSFL5), 9.52% (BSFL10), and 19.06% (BSFL20) (Table 1). Diets were formulated in collaboration with Felleskjøpet Fôrutvikling AS using their optimization least-cost program based on the Dutch energy evaluation system [13]. Diets were formulated on net energy and standardized ileal digestibility (SID) values to be isoenergetic, balanced for digestible amino acids, and to meet or exceed the nutritional requirements for this age pigs [14]. Literature values from Finke [5] for the amino acid content in the BSFL meal were used in the diet formulation. Digestibility coefficients for the amino acids in the BSFL meal were set to 83%. Yttrium oxide (Y2O3) was included as an inert marker in the diets for digestibility calculations. Pelleted diets were produced by the Center for Feed Technology (ForTek, NMBU, Ås, Norway). The feed mash was ground in a Münch hammer mill (HM 21.115, Wuppertal, Germany) fitted with a 3 mm screen before pelleting. The mash was steam conditioned at 82 °C in a double-pass pellet-press conditioner (Münch-Edelstahl, Germany) before pelleting (Münch-Edelstahl, Germany, 2 × 17 kW) through a 3.5 mm die with a production rate of 700 kg/h. The pigs had ad-libitum access to the experimental diets immediately PW through automatic feeders (FRH-2 Domino A/S, Tørring, Denmark) with 43 cm feeding space. The automatic feeders were checked daily and refilled when needed. Feed residues were registered weekly and average daily feed intake (ADFI) per pen was calculated. Clean drinking water was always available from a drinking nipple next to the feeder.
Table 1
Dietary composition of experimental diets, calculated total crude protein (CP) content in diets, and calculated CP and crude fat (CF) from black soldier fly larvae (BSFL) meal.
|
Dietary treatments
|
Ingredients, g/kg as fed
|
Control
|
BSFL5
|
BSFL10
|
BSFL20
|
Wheata
|
507.7
|
502.0
|
496.6
|
485.1
|
Barleyb
|
200.0
|
200.0
|
200.0
|
200.0
|
Oatsc
|
50.0
|
50.0
|
50.0
|
50.0
|
BSFL meald
|
⎯⎯
|
47.6
|
95.2
|
190.6
|
Soybean meale
|
70.8
|
59.7
|
48.2
|
25.5
|
Soy protein concentratef
|
36.1
|
27.1
|
18.1
|
⎯⎯
|
Fish mealg
|
34.1
|
25.5
|
17.1
|
⎯⎯
|
Rapeseed oil
|
32.8
|
25.1
|
17.4
|
1.3
|
AkoFeed Gigant 60h
|
11.0
|
8.1
|
5.1
|
⎯⎯
|
Rapeseed meali
|
10.0
|
10.0
|
10.0
|
10.0
|
Monocalcium phosphate
|
12.9
|
12.0
|
11.2
|
9.5
|
Limestone
|
8.2
|
6.7
|
5.1
|
2.1
|
Sodium chloride
|
5.3
|
5.4
|
5.5
|
5.8
|
Selenium premix
|
0.9
|
0.9
|
0.8
|
0.8
|
Iron(II)fumarate
|
0.4
|
0.4
|
0.4
|
0.4
|
Micro-mineral premixj
|
2.0
|
2.0
|
2.0
|
2.0
|
Vitaminsk
|
3.0
|
3.0
|
3.0
|
3.0
|
L-Lysin
|
6.8
|
6.8
|
6.9
|
6.9
|
L-Methionine
|
2.4
|
2.5
|
2.6
|
2.8
|
L-Threonine
|
2.8
|
2.9
|
2.9
|
3.0
|
L-Valin
|
1.1
|
0.8
|
0.5
|
0.0
|
L-Tryptophan
|
0.9
|
0.8
|
0.7
|
0.6
|
Betaine
|
0.7
|
0.7
|
0.7
|
0.7
|
Yttrium(III)oxide
|
0.1
|
0.1
|
0.1
|
0.1
|
Calculated CP content
|
181.0
|
181.0
|
181.0
|
181.0
|
Ratio CP from BSFL (% of total CP)
|
0
|
10
|
20
|
39
|
Ratio CF from BSFL (% of total CF)
|
0
|
19
|
39
|
69
|
aChemical composition per kg: 867 g DM, 14 g ash, 124 g CP, 488 g starch, 14 g CF, 116 g NDF, 45 g ADF, 16 MJ. |
bChemical composition per kg: 858 g DM, 17 g ash, 92 g CP, 564 g starch, 11 g CF, 206 g NDF, 82 g ADF, 16 MJ. |
cChemical composition per kg: 858 g DM, 23 g ash, 88 g CP, 408 g starch, 44 g CF, 270 g NDF, 150 g ADF, 17 MJ. |
dHiProMine S.A., Poznanska Str, Poland. Chemical composition per kg: 905 g DM, 84 g ash, 380 g CP, 289 g CF, 17.4 g Ca, 2.4 g Mg, 7.8 g total P, 2.7 g. Amino acids per kg: 27.8 g alanine, 16.7 g arginine, 33.2 g aspartic acid, 2.7 g cysteine, 43.8 g glutamic acid, 18.2 g glycine, 9.0 g histidine, 16.4 g isoleucine, 30.4 g leucine, 21.9 g lysine, 6.5 g methionine, 15.0 g phenylalanine, 20.6 g proline, 14.2 g serine, 15.1 g threonine, 20.3 g tyrosine, 21.5 g valine. Lauric acid (C12:0): 86.7 g/kg. |
eNon-GMO soybean meal, Denofa AS, Fredrikstad, Norway. Chemical composition per kg: 876 g DM, 53 g ash, 426 g CP, 11 g CF, 156 g NDF, 128 g ADF, 17 MJ. |
fAX3 Gastric, TripleA a/s, Hornsyld, Denmark. |
gNordsildmel AS, Egersund, Norway. Chemical composition per kg: 920 g DM, 147 g ash, 679 g CP, 101 g CF, 19 MJ. |
hAAK AB, Malmö, Sweden. |
iExpeller-pressed rapeseed cake, Mestilla, UAB, Klaipeda Lithuania. Chemical composition per kg: 928 g DM, 53 g ash, 342 g CP, 100 g CF, 223 g NDF, 179 g ADF, 20 MJ. |
j“Mikro-Svin”; provided per kilogram of diet: 475 mg Ca; 3.4 mg Mg; 13.2 mg S; 120 mg Fe; 60 mg Mn; 120 mg Zn; 26 mg Cu; 0.6 mg I. |
kProvided per kilogram of diet: 0.7 g Vitamin A; 1.2 g Vitamin E v5; 0.8 g Vitamin ADKB mix; 0.3 g Vitamin C (Stay C 35%). |
The farm had an ongoing issue with edema disease and symptoms resulted in antibiotic treatment of five pigs on days 8–10 PW. After one pig died without any registered symptoms on day 11 PW, all pigs were treated with intramuscular antibiotic injections (Borgal vet., Ceva Santé Animale, France) for three consecutive days (11–13 PW). After treatment, all pigs appeared healthy throughout the experiment.
Registrations and sample collection during the experiment
Fecal consistency was assessed daily and registered for all pens based on the four category scale developed by Pedersen and Toft [15]. The daily fecal score was registered as a pen average with 0.25 intervals on the scale. All pigs were weighed weekly and average daily gain (ADG) and feed conversion ratio (FCR) was calculated per pen. Fecal samples were also collected every week for the determination of the fecal DM. An equal amount of feces from each pig was pooled for the pen before oven drying at 103 °C for 24 h. Individual fecal samples were collected on days 21, 22, 25, 26, and 27 for the determination of apparent total tract digestibility (ATTD). Individual samples from all days were pooled, freeze-dried, and ground at 0.5 and 1 mm (Retsch ZM 100 centrifugal mill, Haan, Germany) before chemical analysis. Apparent digestibility of nutrients was calculated as described by Maynard and Loosli [16].
Terminal sample collection
Only pigs from the pens with rubber mats (n = 3 pens per treatment, a total of 47 pigs) were included in the terminal sampling. Pigs were fasting from the evening before but had access to feed three hours before euthanasia. Euthanasia was done using a captive bolt pistol followed by exsanguination. Immediately after exsanguination, the abdominal cavity was opened, and the GIT removed. Intestinal content was collected from the oral part of the jejunum and the top of the colon spiral. Tissue from oral jejunum, aboral ileum, and top of the colon spiral were collected for histological assessment. Intestinal content from the last two meters of the small intestine was collected and stored at -20 °C for the determination of apparent ileal digestibility (AID). This sample was unfortunately not collected from seven of the pigs (three control pigs, two pigs fed BSFL10, and two pigs fed BSFL20). The ileal contents were later freeze-dried, homogenized using a batch mill (A11 basic Analytical mill, IKA®, England) and chemically analyzed. Liver weight was recorded to calculate liver index (liver weight, kg / live body weight, kg * 100).
Table 2
Analyzed chemical composition of dietary treatments.
|
Dietary treatments
|
Nutrients, g/kg DM
|
Control
|
BSFL5
|
BSFL10
|
BSFL20
|
Dry matter, g/kg
|
890.3
|
888.9
|
887.7
|
893.0
|
Ash
|
54.3
|
52.3
|
52.5
|
52.9
|
Crude protein
|
196.8
|
196.1
|
199.8
|
206.8
|
Starch
|
512.5
|
523.8
|
504.1
|
488.0
|
Crude fat
|
69.3
|
79.7
|
78.6
|
89.1
|
NDF
|
124.1
|
122.9
|
118.3
|
131.0
|
ADF
|
52.9
|
52.0
|
50.2
|
53.8
|
Gross energy (MJ/kg)
|
19.5
|
19.6
|
19.8
|
19.9
|
Phosphorus
|
7.4
|
7.3
|
7.6
|
7.0
|
Chemical analyses
Pooled feed samples, collected during the experiment for each diet, were ground at 0.5 and 1 mm (Fritsch Pulverisette 19 cutting mill, Idar-Oberstein, Germany) before the chemical composition of nutrients were analyzed in triplicates. The analyzed chemical composition of the dietary treatments can be found in Table 2. Analyzed amino acid and fatty acid composition of the diets are shown in Table 3 and Table 4, respectively. The chemical analyses were performed by the LabTek group at the Department of Animal and Aquacultural Science, NMBU, Ås, Norway. In brief, DM was determined by drying to constant weight at 103 °C ± 2 °C [17], and ash was determined by complete combustion at 550 °C for at least 4 h [18]. Gross energy (GE) content was determined using a PARR 6400 Automatic Isoperibol Calorimeter (Parr Instruments, Moline, IL, USA) according to ISO 9831 [19]. Crude protein (CP) was analyzed with the Kjeldahl method (AOAC Official Method 2001.11), using a Digestor™ 2520 (FOSS Analytical, Hillerød, Denmark) and the Kjeltec™ 8400 analyzer (FOSS Analytical, Hillerød, Denmark). Crude fat (CF) was analyzed using Accelerated Solvent Extraction (ASE 350, Thermo Fisher Scientific Inc.). Extraction was conducted with 80% petroleum ether and 20% acetone at 125 °C. Starch was determined using an enzymatic-colorimetric method according to McCleary et al. [20], with some modifications. In brief, starch was degraded with heat-stable α-amylase and amyloglucosidase-enzymes to glucose. Glucose concentration was then determined using a spectrophotometer (RX Daytona +, Randox Laboratories Ltd., UK). Acid detergent fiber (ADF) and neutral detergent fiber (NDF) were analyzed according to the manufacturer’s methods using the Ankom200 Fiber Analyzer (ANKOM Technology, Macedon, New York, USA). Amino acids in diets and ileal samples were analyzed according to Commission Regulation (EC) No 152/2009. Amino acids were analyzed on a Biochrom 30 + Amino Acid Analyzer with an autosampler (Biochrom Ltd., Cambridge, UK). Tryptophan was analyzed in diets on a Dionex Ultimate 3000 HPLC system (Dionex Softron GmbH, Germering, Germany) with a Shimadzu RF-535 fluorescence detector (Shimadzu Corporation, Kyoto, Japan). The fatty acid composition of the diets was analyzed according to O'fallon et al. [21] by synthesizing the fatty acids to fatty acid methyl esters (FAME), in which concentrations were determined using a Trace GC Ultra gas chromatograph (Thermo Fisher Scientific, US). Total phosphorus was analyzed after combustion and acid digestion (Commission Regulation (EC) No 152/2009) using a commercial spectrophotometric kit (PH8328, Randox laboratories, County Antrim, UK). Yttrium concentration was determined after acid decomposition in a microwave digestion system (Start D, Milestone Srl, Italy), using a microwave plasma atomic emission spectrometer (MP-AES 4200, Agilent Technologies, US).
Table 3
Analyzed amino acid composition of dietary treatments.
|
Dietary treatments
|
Indispensable AA, g/16 g Na
|
Control
|
BSFL5
|
BSFL10
|
BSFL20
|
Arginine
|
4.9
|
4.9
|
4.6
|
4.2
|
Histidine
|
2.1
|
2.2
|
2.2
|
2.3
|
Isoleucine
|
3.2
|
3.3
|
3.2
|
3.3
|
Leucine
|
6.0
|
6.0
|
5.9
|
5.9
|
Lysine
|
6.7
|
7.2
|
6.6
|
6.9
|
Methionine
|
2.3
|
2.4
|
2.3
|
2.5
|
Phenylalanine
|
3.8
|
3.7
|
3.6
|
3.8
|
Threonine
|
4.1
|
4.3
|
4.0
|
4.3
|
Tryptophan
|
1.4
|
1.2
|
1.4
|
1.4
|
Valine
|
4.0
|
4.1
|
3.9
|
4.1
|
Dispensable AA, g/16 g N
|
|
|
|
|
Alanine
|
3.3
|
3.6
|
3.7
|
4.1
|
Aspartic acid
|
6.8
|
6.9
|
6.5
|
6.4
|
Cysteine
|
1.3
|
1.3
|
1.2
|
1.1
|
Glutamic acid
|
19.9
|
19.1
|
18.7
|
18.2
|
Glycine
|
3.3
|
3.4
|
3.3
|
3.3
|
Proline
|
5.9
|
5.9
|
6.0
|
6.3
|
Serine
|
3.7
|
3.7
|
3.6
|
3.5
|
Tyrosine
|
1.7
|
1.9
|
2.2
|
3.1
|
Total amino acids, g/16 g N
|
83.1
|
83.8
|
81.6
|
83.5
|
aDetermined using water-corrected molecular weights |
Table 4
Analyzed fatty acid composition of dietary treatments, and calculated sum of saturated-, monounsaturated-, and polyunsaturated fatty acids.
|
Dietary treatments
|
Fatty acids, g/kg DM
|
Control
|
BSFL5
|
BSFL10
|
BSFL20
|
C12:0
|
0.40
|
6.11
|
11.7
|
23.1
|
C14:0
|
0.42
|
1.35
|
2.33
|
4.25
|
C15:0
|
0.04
|
0.06
|
0.07
|
0.09
|
C16:0
|
13.3
|
12.4
|
11.4
|
9.96
|
C17:0
|
0.07
|
0.08
|
0.10
|
0.13
|
C18:0
|
4.31
|
3.49
|
2.76
|
1.54
|
C20:0
|
0.24
|
0.20
|
0.15
|
0.09
|
C21:0
|
0.01
|
0.09
|
0.28
|
0.32
|
C22:0
|
0.14
|
0.11
|
0.08
|
0.04
|
C23:0
|
0.02
|
0.01
|
0.01
|
-
|
C24:0
|
0.05
|
0.04
|
0.03
|
0.02
|
Sum saturated fatty acids
|
19.02
|
23.95
|
28.89
|
39.57
|
C14:1
|
-
|
0.02
|
0.04
|
0.08
|
C16:1
|
0.40
|
0.58
|
0.76
|
1.13
|
C20:1
|
0.89
|
0.73
|
0.55
|
0.22
|
C24:1
|
0.11
|
0.08
|
0.04
|
0.03
|
Sum monounsaturated fatty acids
|
1.40
|
1.41
|
1.39
|
1.46
|
C18:1n9t
|
0.46
|
0.37
|
0.21
|
0.04
|
C18:1n9c
|
25.9
|
22.8
|
19.0
|
12.2
|
C18:2n6c
|
21.1
|
22.0
|
21.7
|
21.1
|
C18:3n3
|
4.56
|
4.15
|
3.56
|
2.39
|
C18:3n6
|
0.13
|
0.11
|
0.08
|
0.02
|
C20:2
|
0.13
|
0.11
|
0.09
|
0.05
|
C20:4n6
|
0.02
|
0.02
|
0.01
|
-
|
C20:5n3
|
0.30
|
0.23
|
0.16
|
-
|
C21:1n9
|
0.05
|
0.05
|
0.04
|
0.02
|
C22:2
|
0.04
|
0.02
|
0.02
|
0.02
|
C22:5n3
|
0.03
|
0.02
|
0.01
|
-
|
C22:6n3
|
0.36
|
0.30
|
0.20
|
-
|
Sum polyunsaturated fatty acids
|
53.06
|
50.17
|
45.04
|
35.89
|
Trypsin and lipase activities were analyzed in jejunal content. 1.5 ml (600 µl for lipase analysis) ice-cold Milli-Q water were added to approximately 100 mg of the jejunal content, homogenized using a bead mill (TissueLyser, Qiagen Retsch, Haan, Germany) and sonicated in an ice-cold bath for three minutes (T 460/H, Elma Schmidbauer GmbH, Ransbach-Baumbach, Germany). After centrifugation at 21,100 × g for 10 min at 4 °C, the supernatant was collected, aliquoted, stored at -80 °C, and used for the analysis of lipase, trypsin, and total protein. Total protein concentration was determined in microtiter assay according to the Quick Start™ Bradford Protein Assay protocol (Bio-Rad Laboratories, Oslo, Norway). Absorbance was measured using a SpectraMax M2e Microplate Reader (Molecular Devices, LLC., San Jose, USA). Lipase and trypsin activity were analyzed using commercial kits (Lipase Activity Assay Kit III, MAK048-1KT, fluorometric, Sigma-Aldrich, Merck KGaA; Trypsin Activity Assay Kit, ab102531, colorimetric, Abcam), according to the manufacturer’s protocols.
Short-chain fatty acids (SCFA) were analyzed in colon content. Samples were thawed on ice and 500 mg of the colon content were mixed with 500 µl ice-cold internal standard solution (2-methyl valeric acid in 5% formic acid), before sonication for 5 min in cold water. After centrifugation for 15 min at 4 °C with 15000 × g, the supernatant was transferred to a spin column (45 kDa; VWR International, USA), and again centrifuged with the same parameters. SCFA concentration was determined by capillary gas chromatography on a stabilwax-DA, 30 m × 0.25 mm × 0.25 µm capillary column (Restek corporation, PA, USA) installed on a Trace 1300 gas chromatograph equipped with an AS 1310 autosampler, split injection, a flame ionization detector and Chromeleon software (Thermo Scientific, MA, USA). The initial oven temperature was 90 °C, held for 2 min, followed by a temperature increase of 10 °C/min to 150 °C and 50 °C/min to 250 °C and then held for 1 min. Helium was used as the carrier gas at a flow rate of 3 mL/min. The injector temperature was set at 260 °C and the detector temperature was set at 275 °C.
Morphology and morphometry
Jejunal, ileal, and colon morphology were blindly assessed and villus heights (VH) and crypt depths (CD) measured by Aquamedic AS, Oslo, Norway. Gross pathological observations were recorded before tissue sampling. Samples were fixated in 10% formalin up to 48 h before processing following standard histological methods for gut tissue. Sections were stained with hematoxylin and eosin (H&E) and evaluated by light microscopy, where the evaluation was done on morphological characteristics such as epithelial cell and barrier morphology and integrity, crypt changes such as hyperplasia, dilation or abscessation, degenerative and inflammatory mucosal changes including increased numbers of intraepithelial lymphocytes (IELs) and infiltration by leucocytes. Methodologies of the evaluation protocol are described by Day et al. [22] and Pérez de Nanclares et al. [23]. The morphological characteristics evaluated were graded using a semi-quantitative scoring system where score 0 is normal, score 1 represent mild changes, and score 2, 3, and 4 represent moderate, marked, and severe changes, respectively. VH and CD measurements were made on scanned whole-section images of the respective tissues captured using the PreciPoint M8 Microscope and Scanner (PreciPoint, Freising, Germany), and obtained using the ViewPoint software (PreciPoint, Freising, Germany). A minimum of three well-oriented crypts and villi were measured from each of the sections.
Extraction of DNA and 16S rRNA sequencing
Total DNA was extracted from bacteria in approximately 190 mg of colon content using QIAamp Fast DNA Stolen Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s guidelines. The DNA concentration was determined using NanoDrop™ 8000 spectrophotometer (Thermo Fisher Scientific, Waltham, Massachusetts, USA). All samples were stored at -20 ºC until further analysis. Before preparing for 16S rRNA sequencing, samples were normalized to 10 ng/µL. The V3-V4 regions of the bacterial 16S rRNA gene were amplified using the primers Pro341f (5'-CCTACGGGNBGCASCAG-3') and Pro805r (5'-GACTACNVGGGTATCTAATCC-3'). The library preparation was conducted using the Miseq Reagent Kit V3 (Illumina, San Diego, California, USA) according to the Illumina 16 S Metagenomic Sequencing Library Preparation protocol (Illumina, San Diego, California, USA). For indexing, Nextera XT index kit V2 was used (Illumina, San Diego, California, USA). After the indexing reaction, all samples were measured by Qubit Fluorometer (Invitrogen, Carlsbad, California, USA) using Qubit™ 1X dsDNA HS Assay Kit (Invitrogen, Carlsbad, California, USA). An equal amount of each sample was pooled together, and spiked with 5% PhiX Control (Illumina, San Diego, Waltham, MA, USA). For sequencing, 10 pm of the pooled sample was loaded to a flow cell. The sequencing analysis was performed on the Miseq System (Illumina, San Diego, California, USA). The clustering density was 1256 k/mm2 and 88.3% of clusters were passing filter.
Raw sequence data were analyzed using DADA2 v. 1.12.1 [24] in R v. 3.5.0 [25]. Default parameters were used if other is not specified. In brief, primers were removed, and the forward reads were truncated at 280 bp and the reverse reads at 250 bp. Max expected errors were set to 7. This allowed 73% of the reads to pass the quality control. Error rates were estimated, and the core sample inference algorithm applied. The denoised read pairs were merged, and chimeras removed. The Silva v. 138 database [26, 27] was used as a reference database for the taxonomy assignment. A phyloseq object was built with the phyloseq v.1.26.1 for further analyses [28]. Figures were made with ggplot2 v.3.2.1 [29].
Statistical analysis
Outliers in the data were identified using the interquartile range (IQR) method. Outliers were defined as > Q3 + 3* IQR or < Q1 + 3*IQR. Statistical analysis was performed using R v.3.6.1 [25] in Rstudio v.1.2.5001 [30]. A mixed procedure was run, using the lme4 1.1–21 [31] and lmerTest 3.1-1 [32] packages. The following model was used for all individual data: Yijklmn = µ + dieti + sexj + beddingk + litterl + penm + εijklmn where Y is one observation on pig n; µ is the intercept; dieti is the fixed dietary treatment effect (i = 1:4); sexj is the fixed effect of the sex of the pig (j = 1,2); beddingk is the fixed effect of bedding material, rubber mat or wood shavings (k = 0,1); litterl is the random effect of the lth litter (l = 1:11); penm is the random effect of the pen (m = 1:20) and εijklmn is a random residual. The bedding was not included in the model when analyzing the terminal sampling parameter, as it was constant. For all pen-level parameters, the following model was used with the lm function in the stats package [25]: Yikn = µ + dieti + beddingk + εn where Y now is one observation on pen n. Results are presented as mean values and standard error of the mean (SEM). In addition, linear regression with the dietary inclusion level of BSFL as the only explanatory variable was run with the lm function for all dependent variables. For the effects of sex and bedding material, only significant results are presented. Effects are considered statistically significant when P ≤ 0.05 and tendencies are defined as P-values between 0.05 and 0.10.
To assess diversity in the microbial communities within pigs, Shannon alpha-diversity indices were calculated at the amplicon sequence variant (ASV) level. A comparison of the Shannon indices between dietary treatments was done using the Kruskal-Wallis Rank Sum Test in the stats package [25]. The beta-diversity (between pig variation in microbial communities) was assessed by principal coordinate analyses (PCoA) with the Bray-Curtis, unweighted, and weighted UniFrac distance matrices. Beta dispersion (variances) was calculated within each dietary group and a permutation-based test of multivariate homogeneity applied (vegan package v.2.6-6; Oksanen et al. [33]). Fulfilling the assumption of homogeneity in group variance, a PERMANOVA test was performed on the distance matrices with the dietary group as the independent variable. Pairwise PERMANOVA tests were performed to compare beta diversity between dietary treatments. P-values were adjusted for multiple testing with the method by Benjamini and Hochberg [34], also known as the false discovery rate.
The relative abundance was calculated, and the statistical difference in relative abundance between dietary treatments was analyzed with the Kruskal-Wallis test with dietary treatment as the explanatory variable.
To test for a statistical difference in relative abundance between dietary treatments, the Kruskal-Wallis test with dietary treatment as the explanatory variable was applied. Two-sample Wilcoxon tests, also known as the Mann-Whitney test, was used for pairwise comparison between the diets if the Kruskal Wallis test gave a significant effect of dietary treatment. P-values were corrected for multiple testing with the Benjamini and Hochberg [34] method.
To test for covariation between the microbiota and SCFA profile, dissimilarity indices with the Bray-Curtis indices were calculated separately for the microbiota and SCFA data with the vegdist function, and the covariation tested with the mantel function in the vegan package [33].